Temporally Correlated Active Noise Simulation Tutorial¶
Temporally Correlated Active Noise Simulation is available in OpenMichroM versions >= 1.0.7
Introduction¶
This tutorial is aimed at introducing nonequilibrium activity to OpenMiChroM simulations. First, we will go through a very brief introduction of the theoretical idea, then, the simulation procedures are discussed.
Theory¶
Activity, such as originating from molecular motors applying forces on the polymer, is modeled as an athermal drive experienced by each coarse-grained monomer. Since motors typically exhibit on/off dynamics, the athermal force is expected to be correlated in time, as opposed to the thermal noise that is temporally uncorrelated. To model activity, we add a novel noise-like term to the forces associated with a monomer, such that the equation of motion of the \(n\)-th monomer reads as follows:
\[\gamma \frac{dr_n}{dt} = -\nabla_n U + \xi^{\rm therm}_n + f^{\rm act}_n\]
where \(\gamma\) is the damping coefficient and \(U\) is the passive potential, like the harmonic bonds joining neighboring monomers in a polymer. \(\xi^{\rm therm}_n\) is the the thermal noise that is uncorrelated over time as well as across the chain:
\[\langle \xi^{\rm therm}_n(t)\rangle=0\quad \text{and} \quad \langle \xi^{\rm therm}_n(t)\xi^{\rm therm}_m(t^\prime)\rangle = 2\gamma T\delta_{mn}\delta(t-t^\prime).\]
The active noise kicks are given by \(f^{\rm act}(t)\), which are correlated over time and their correlation decays over a characteristic time scale \(\tau\):
\[\langle f^{\rm act}_n \rangle=0 \quad \text{and} \quad \langle f^{\rm act}_n(t)f^{\rm act}_m(t^\prime) \rangle=F^2e^{-|t-t^\prime|/\tau}\delta_{mn}\]
The dynamics of the active force of the \(n\)-th monomer is governed by the following equation:
\[\tau \frac{df^{\rm act}_n}{dt} = -f^{\rm act}_n + \sqrt{2\gamma \theta_a}\eta(t)\]
where \(\theta_a\equiv F^2\tau/\gamma\) is the active temperature-like quantity, and \(\eta(t)\) is a delta-correlated stationary Gaussian process.
Brownian Dynamics¶
Brownian dynamics only has forces and displacements, and no velocities. The positions after time \(\Delta t\), given by \(x(t+\Delta t)\) are computed based on the current forces \(h(t)\) and positions \(x(t)\).
\[x_n(t+\Delta t)=x_n(t)+\frac{h_n(t)}{\gamma}\Delta t+\sqrt{\frac{2T}{\gamma}\Delta t}\mathcal{N}(0,1)\]
where the last term is the thermal kick at temperature \(T\) with \(\mathcal{N}(0,1)\) representing a random Normal variable with zero mean and unit standard deviation. The net force experienced by the \(n\)-th monomer at time step \(t\) is given by \(h_n(t)\).
\[h_n(t)= -\frac{\partial}{\partial x}\sum_{m}U(|x_n(t)-x_m(t)|)+f^{\rm act}_n(t)\]
The net force for a monomer \(h(t)\), depends on the active force of the monomer \(f^{\rm act}(t)\), which is related to the active force in the previous time step \(f^{\rm act}(t-\Delta t)\). The active force on the \(n\)-th monomer at time \(t\) is obtained as follows:
\[f^{\rm act}_n(t)=f^{\rm act}_n(t-\Delta t)e^{-\Delta t/\tau}+{F}\sqrt{1-e^{-2\Delta t/\tau}}\mathcal{\tilde{N}}(0,1)\]
where \(\mathcal{\tilde{N}}(0,1)\) is a random Normal variable that is different from the thermal one.
Next is a step-by-step guidance on how to setup and run OpenMiChroM simulations with correlated active noise. Users not familiar with running OpenMiChroM simulations, would greatly benefit from first going through the practice of running equilibrium OpenMiChroM simulations - see Tutorial_Single_Chromosome. For users already familiar with OpenMiChroM, it is still the same simulation object that is created and basic steps of running the simulations are the same. The main differences are two fold: 1. Adding activity using a function addCorrelatedNoise(). One should make sure to add activity as the first force field. It is extremely important that the active force is assigned a force-group “0”. 2. Using a custom integrator ActiveBrownianIntegrator (see Integrator.py) that takes care of the active force which is hard-coded to be the force-group “0”. Hence the catutionary statement above.
Hope you follow along!
Simulations¶
Import modules¶
Active functions are
[1]:
import sys
sys.path.append('../../OpenMiChroM/')
from ChromDynamics import MiChroM
from Integrators import ActiveBrownianIntegrator
import numpy as np
Initialize simulation¶
[2]:
# Instantiate MiChroM object
sim = MiChroM(name='active_Rouse_sim', temperature=0.2, time_step=0.001, collision_rate=1.0)
# specify platform and output destination
sim.setup(platform="opencl")
sim.saveFolder('./out')
active_correaltion_time = 5.0
#specify the integrator for correlated noise
#note that the force-group "0" is associated with the correlated active noise
sim.integrator = ActiveBrownianIntegrator(timestep=sim.timestep, temperature=sim.temperature,
collision_rate=sim.collisionRate, corr_time=active_correaltion_time)
***************************************************************************************
**** **** *** *** *** *** *** *** OpenMiChroM-1.0.6 *** *** *** *** *** *** **** ****
OpenMiChroM is a Python library for performing chromatin dynamics simulations.
OpenMiChroM uses the OpenMM Python API,
employing the MiChroM (Minimal Chromatin Model) energy function.
The chromatin dynamics simulations generate an ensemble of 3D chromosomal structures
that are consistent with experimental Hi-C maps, also allows simulations of a single
or multiple chromosome chain using High-Performance Computing
in different platforms (GPUs and CPUs).
OpenMiChroM documentation is available at https://open-michrom.readthedocs.io
OpenMiChroM is described in: Oliveira Junior, A. B & Contessoto, V, G et. al.
A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes.
Journal of Molecular Biology. doi:10.1016/j.jmb.2020.10.034.
and
Oliveira Junior, A. B. et al.
Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal.
J. Phys. Chem. B, doi:10.1021/acs.jpcb.1c04174.
Copyright (c) 2022, The OpenMiChroM development team at
Rice University
***************************************************************************************
Load initial structure¶
[3]:
# generate a test sequence file of size n
n=10
with open('test_seq.txt','w') as seq_file:
for ii in range(n):
seq_file.write(f'{ii+1} A1\n')
# create a random configuration with the sequence file
init_struct = sim.createRandomWalk(ChromSeq='test_seq.txt')
sim.loadStructure(init_struct, center=True)
#uncomment below to save the loaded structure
# sim.saveStructure(mode = 'auto')
Add forces¶
[4]:
# For the purpose of the simualtion we will consider a simple simulation of an active Rouse chain - harmonically bonded monomers with zero rest length
# the good things about active Rouse chain is that the dynamics may be calculated analytically and compared for verification.
# Any force-field available for OpenMiChroM, like self-avoidance, may be used.
# However, since Brownian Dynamics does not have momentum, it is prudent to make sure the time step is small enough for steep potentials.
# Using too large a time step with steep (or worse, diverging!) potentials will generate huge forces, possibly leading to explosion! wear your safety goggles!
# Now the force-fields:
# first, add correlated noise.
# IMPORTANT: correlated noise should always be added as the *first* force-field.
# This is because force-group "0" is hard-coded as the active force within ActiveBrownianIntegrator
# act_seq contains the active force values F for each monomer. It needs to be the same size as the total number of monomers
# the values F_i in the list need not be the same, they can be heterogenous depicting varied motor activity
# below we consider a homogenously active polymer
F = 0.5
sim.addCorrelatedNoise(act_seq=F*np.ones(sim.N))
# add Harmonic bonds between monomers of the chain. Use sim.chains to get the number of chains.
# setting the rest length to zero since the analytical form is easier to calculate that way.
kb=5.0
sim.addHarmonicBonds(kfb=kb, r0=0.0)
# adding soft-core self-avoidance
# repulsion is modeled using a sigmoid function with a finite overlap energy Ecut
# sim.addSelfAvoidance(Ecut=4.0, k_rep=20.0, r0=1.0)
# half-harmonic restraint as confinement
# sim.addFlatBottomHarmonic(kr=10.0, n_rad=20.0)
==================================
Active Monomers (correlated noise) added.
Active correlation time: 5.0
Total number of active monomers: 10
Total number of monomers: 10
==================================
Run intial collapse¶
[5]:
#run collapse simulation
for _ in range(10):
sim.runSimBlock(3000, increment=False)
# save the collapsed structure -- uncomment below
# sim.saveStructure(filename='collapse',mode='ndb')
Number of exceptions: 9
adding force ActiveForce 0
adding force HarmonicBond 1
Positions...
loaded!
potential energy is 2.250014
bl=0 pos[1]=[-0.1 -0.6 0.4] dr=1.67 t=3.0ps kin=5.53 pot=0.39 Rg=0.631 SPS=7171
bl=0 pos[1]=[0.5 -1.6 1.8] dr=1.64 t=6.0ps kin=4.23 pot=-0.36 Rg=0.610 SPS=8611
bl=0 pos[1]=[0.7 -2.8 1.5] dr=0.99 t=9.0ps kin=2.77 pot=-0.19 Rg=0.699 SPS=8800
bl=0 pos[1]=[1.7 -2.8 1.7] dr=1.10 t=12.0ps kin=3.35 pot=-0.50 Rg=0.923 SPS=8863
bl=0 pos[1]=[2.2 -2.3 2.6] dr=0.86 t=15.0ps kin=2.37 pot=-0.70 Rg=0.530 SPS=8788
bl=0 pos[1]=[1.7 -2.6 3.0] dr=0.75 t=18.0ps kin=3.77 pot=-0.62 Rg=0.517 SPS=8933
bl=0 pos[1]=[1.6 -1.6 3.6] dr=1.13 t=21.0ps kin=3.43 pot=-0.39 Rg=0.972 SPS=8865
bl=0 pos[1]=[1.3 -2.0 3.1] dr=1.29 t=24.0ps kin=3.95 pot=0.10 Rg=0.891 SPS=8965
bl=0 pos[1]=[1.2 -3.6 1.4] dr=1.26 t=27.0ps kin=5.72 pot=0.83 Rg=0.717 SPS=8999
bl=0 pos[1]=[1.5 -4.1 1.2] dr=0.63 t=30.0ps kin=3.92 pot=0.74 Rg=0.530 SPS=9082
Run simulation¶
[6]:
# For the purpose of the tutorial we will just store the data in the xyz array for plotting
# you may instead save the data into cndb/ndb/pdb files and load into numpy arrays using cndbtools
# if you would like to save the data uncomment the lines below
# sim.initStorage(filename="active_Rouse_sim"") # initiate storage
xyz = [sim.getPositions()]
n_blocks = 500 # number of simulation blocks
block_size = 1000 # size of each block
for _ in range(int(n_blocks)):
sim.runSimBlock(int(block_size), increment=True)
# sim.saveStructure()
xyz.append(sim.getPositions())
# sim.saveStructure(filename='lastframe',mode='ndb')
# sim.storage[0].close()
xyz = np.array(xyz)
print(xyz.shape) # the shape should be: (number of blocks, number of monos, deg. of freedom)
bl=1 pos[1]=[1.3 -5.0 1.1] dr=0.62 t=31.0ps kin=2.41 pot=0.79 Rg=0.588 SPS=7621
bl=2 pos[1]=[1.6 -4.5 1.2] dr=0.61 t=32.0ps kin=3.50 pot=0.55 Rg=0.624 SPS=7894
bl=3 pos[1]=[1.1 -5.2 1.3] dr=0.68 t=33.0ps kin=3.32 pot=0.83 Rg=0.890 SPS=8432
bl=4 pos[1]=[1.0 -4.6 1.3] dr=0.60 t=34.0ps kin=3.93 pot=1.05 Rg=0.706 SPS=8478
bl=5 pos[1]=[0.9 -5.4 1.2] dr=0.64 t=35.0ps kin=2.70 pot=1.35 Rg=0.897 SPS=8574
bl=6 pos[1]=[1.5 -5.2 1.3] dr=0.66 t=36.0ps kin=3.38 pot=0.93 Rg=0.774 SPS=8658
bl=7 pos[1]=[1.9 -5.3 1.8] dr=0.62 t=37.0ps kin=2.75 pot=0.97 Rg=0.833 SPS=8889
bl=8 pos[1]=[2.0 -5.1 2.3] dr=0.53 t=38.0ps kin=3.94 pot=0.70 Rg=0.517 SPS=8786
bl=9 pos[1]=[1.8 -5.4 2.4] dr=0.54 t=39.0ps kin=3.99 pot=0.69 Rg=0.544 SPS=8805
bl=10 pos[1]=[1.6 -5.9 3.1] dr=0.75 t=40.0ps kin=2.92 pot=0.54 Rg=0.468 SPS=8681
bl=11 pos[1]=[2.1 -6.0 3.2] dr=0.71 t=41.0ps kin=1.58 pot=0.87 Rg=0.451 SPS=8699
bl=12 pos[1]=[2.5 -6.8 3.3] dr=0.78 t=42.0ps kin=2.89 pot=0.69 Rg=0.360 SPS=8515
bl=13 pos[1]=[2.0 -6.6 3.4] dr=0.81 t=43.0ps kin=2.64 pot=0.81 Rg=0.444 SPS=8633
bl=14 pos[1]=[1.7 -7.1 3.2] dr=0.52 t=44.0ps kin=2.34 pot=1.00 Rg=0.476 SPS=8597
bl=15 pos[1]=[1.8 -6.6 3.3] dr=0.90 t=45.0ps kin=2.82 pot=1.51 Rg=0.600 SPS=8924
bl=16 pos[1]=[1.9 -6.9 2.9] dr=0.59 t=46.0ps kin=2.70 pot=2.04 Rg=0.533 SPS=8925
bl=17 pos[1]=[1.7 -6.3 2.3] dr=0.65 t=47.0ps kin=2.17 pot=2.08 Rg=0.623 SPS=8774
bl=18 pos[1]=[0.7 -7.1 2.6] dr=0.72 t=48.0ps kin=2.32 pot=1.98 Rg=0.651 SPS=8284
bl=19 pos[1]=[1.5 -7.2 3.0] dr=0.73 t=49.0ps kin=2.22 pot=1.70 Rg=0.239 SPS=8612
bl=20 pos[1]=[1.0 -7.7 3.5] dr=0.57 t=50.0ps kin=2.30 pot=1.83 Rg=0.368 SPS=8729
bl=21 pos[1]=[1.1 -7.5 4.5] dr=0.73 t=51.0ps kin=1.98 pot=1.71 Rg=0.629 SPS=8843
bl=22 pos[1]=[1.1 -7.6 4.4] dr=0.45 t=52.0ps kin=2.86 pot=1.61 Rg=0.725 SPS=8919
bl=23 pos[1]=[1.1 -7.6 3.6] dr=0.61 t=53.0ps kin=2.89 pot=1.53 Rg=0.522 SPS=8702
bl=24 pos[1]=[1.0 -7.3 3.9] dr=0.54 t=54.0ps kin=3.78 pot=1.54 Rg=0.455 SPS=8720
bl=25 pos[1]=[0.6 -7.3 4.2] dr=0.45 t=55.0ps kin=2.99 pot=1.53 Rg=0.688 SPS=8669
bl=26 pos[1]=[0.5 -7.1 3.8] dr=0.66 t=56.0ps kin=2.67 pot=2.00 Rg=0.691 SPS=8478
bl=27 pos[1]=[-0.1 -7.4 3.1] dr=0.54 t=57.0ps kin=2.49 pot=2.12 Rg=0.597 SPS=8733
bl=28 pos[1]=[0.3 -7.0 3.3] dr=0.64 t=58.0ps kin=2.04 pot=2.53 Rg=0.507 SPS=8880
bl=29 pos[1]=[-0.3 -7.2 3.7] dr=0.70 t=59.0ps kin=1.81 pot=2.13 Rg=0.478 SPS=8714
bl=30 pos[1]=[-0.4 -7.2 4.2] dr=0.67 t=60.0ps kin=2.98 pot=2.15 Rg=0.691 SPS=8777
bl=31 pos[1]=[0.3 -6.7 3.6] dr=0.72 t=61.0ps kin=2.48 pot=1.79 Rg=0.390 SPS=8590
bl=32 pos[1]=[0.2 -7.0 3.9] dr=0.38 t=62.0ps kin=2.82 pot=1.92 Rg=0.525 SPS=8689
bl=33 pos[1]=[0.6 -6.5 4.0] dr=0.53 t=63.0ps kin=3.03 pot=1.82 Rg=0.580 SPS=8618
bl=34 pos[1]=[0.6 -6.5 3.7] dr=0.43 t=64.0ps kin=2.71 pot=1.54 Rg=0.350 SPS=8732
bl=35 pos[1]=[0.2 -6.7 4.1] dr=0.57 t=65.0ps kin=3.25 pot=1.40 Rg=0.499 SPS=8902
bl=36 pos[1]=[0.7 -6.5 4.1] dr=0.78 t=66.0ps kin=2.26 pot=1.13 Rg=0.321 SPS=8771
bl=37 pos[1]=[0.5 -6.4 4.0] dr=0.50 t=67.0ps kin=1.75 pot=1.21 Rg=0.413 SPS=9004
bl=38 pos[1]=[0.3 -6.7 4.4] dr=0.48 t=68.0ps kin=2.10 pot=1.08 Rg=0.365 SPS=8660
bl=39 pos[1]=[0.2 -7.4 4.6] dr=0.72 t=69.0ps kin=2.33 pot=0.99 Rg=0.518 SPS=8627
bl=40 pos[1]=[0.9 -7.0 5.2] dr=0.87 t=70.0ps kin=2.63 pot=0.42 Rg=0.360 SPS=8620
bl=41 pos[1]=[1.4 -6.8 4.5] dr=0.67 t=71.0ps kin=2.64 pot=0.52 Rg=0.528 SPS=8807
bl=42 pos[1]=[0.7 -5.8 5.3] dr=0.73 t=72.0ps kin=3.55 pot=0.47 Rg=0.452 SPS=8790
bl=43 pos[1]=[0.6 -5.9 6.2] dr=0.79 t=73.0ps kin=3.02 pot=0.61 Rg=0.568 SPS=8901
bl=44 pos[1]=[0.0 -6.3 5.2] dr=0.81 t=74.0ps kin=3.40 pot=1.12 Rg=0.557 SPS=8937
bl=45 pos[1]=[-0.1 -7.4 5.6] dr=0.80 t=75.0ps kin=2.41 pot=1.57 Rg=0.484 SPS=8856
bl=46 pos[1]=[-1.1 -7.2 5.3] dr=0.75 t=76.0ps kin=4.20 pot=1.90 Rg=0.425 SPS=8737
bl=47 pos[1]=[-1.5 -7.3 4.7] dr=0.86 t=77.0ps kin=6.58 pot=2.32 Rg=0.405 SPS=8678
bl=48 pos[1]=[-1.7 -7.1 4.2] dr=0.90 t=78.0ps kin=5.83 pot=2.99 Rg=0.470 SPS=8809
bl=49 pos[1]=[-2.5 -7.0 4.0] dr=0.78 t=79.0ps kin=6.04 pot=3.31 Rg=0.555 SPS=8671
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [-2.5260031 -7.63105731 4.11936607] Rg = 0.555199
median bond size is 0.2993247084597079
three shortest/longest (<10)/ bonds are [0.0619413 0.18132575 0.26687537] [0.48378056 0.48624118 0.52440487]
95 percentile of distance to center is: 0.7736948328496079
density of closest 95% monomers is: 4.896952672744252
density of the core monomers is: 5.717321659637082
min/median/mean/max coordinates are:
x: -2.93, -2.53, -2.53, -2.17
y: -8.26, -7.68, -7.63, -7.01
z: 3.84, 4.10, 4.12, 4.60
Statistics for velocities:
mean kinetic energy is: 6.038497269500298 should be: 1.5
fastest particles are (in kT): [ 4.12132149 7.91483392 8.78585725 10.29837843 17.11273306]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 3.3082054138183596
bl=50 pos[1]=[-2.4 -6.7 4.2] dr=0.84 t=80.0ps kin=5.53 pot=3.82 Rg=0.769 SPS=8882
bl=51 pos[1]=[-3.4 -7.3 4.4] dr=0.75 t=81.0ps kin=3.60 pot=4.06 Rg=0.507 SPS=8752
bl=52 pos[1]=[-3.3 -8.0 3.4] dr=1.18 t=82.0ps kin=2.91 pot=4.97 Rg=0.629 SPS=8653
bl=53 pos[1]=[-4.1 -7.9 3.5] dr=0.57 t=83.0ps kin=2.69 pot=4.81 Rg=0.584 SPS=8691
bl=54 pos[1]=[-3.8 -8.8 3.6] dr=0.53 t=84.0ps kin=3.32 pot=4.78 Rg=0.494 SPS=8960
bl=55 pos[1]=[-3.7 -9.5 3.0] dr=0.63 t=85.0ps kin=3.45 pot=5.15 Rg=0.389 SPS=8810
bl=56 pos[1]=[-3.2 -8.6 2.2] dr=0.80 t=86.0ps kin=2.76 pot=5.04 Rg=0.580 SPS=8745
bl=57 pos[1]=[-3.2 -8.5 1.7] dr=0.60 t=87.0ps kin=1.64 pot=5.17 Rg=0.476 SPS=8836
bl=58 pos[1]=[-2.8 -8.5 2.3] dr=0.54 t=88.0ps kin=3.29 pot=5.08 Rg=0.562 SPS=8871
bl=59 pos[1]=[-2.6 -8.1 2.3] dr=0.68 t=89.0ps kin=2.82 pot=4.93 Rg=0.351 SPS=8918
bl=60 pos[1]=[-2.8 -7.6 1.6] dr=0.66 t=90.0ps kin=3.23 pot=4.73 Rg=0.450 SPS=8534
bl=61 pos[1]=[-2.2 -7.6 1.2] dr=0.69 t=91.0ps kin=2.43 pot=4.52 Rg=0.618 SPS=8722
bl=62 pos[1]=[-1.6 -6.9 1.7] dr=0.65 t=92.0ps kin=2.53 pot=4.52 Rg=0.731 SPS=8448
bl=63 pos[1]=[-1.8 -6.9 1.1] dr=0.65 t=93.0ps kin=3.41 pot=4.43 Rg=0.776 SPS=7700
bl=64 pos[1]=[-2.4 -6.4 1.1] dr=0.69 t=94.0ps kin=4.03 pot=4.38 Rg=0.718 SPS=7988
bl=65 pos[1]=[-1.7 -6.0 0.9] dr=0.61 t=95.0ps kin=3.88 pot=4.20 Rg=0.679 SPS=7884
bl=66 pos[1]=[-1.2 -6.3 0.8] dr=0.46 t=96.0ps kin=3.68 pot=4.46 Rg=0.591 SPS=7482
bl=67 pos[1]=[-1.8 -5.9 1.5] dr=0.83 t=97.0ps kin=3.63 pot=4.16 Rg=0.717 SPS=7743
bl=68 pos[1]=[-2.3 -5.9 1.2] dr=0.75 t=98.0ps kin=4.69 pot=4.26 Rg=0.497 SPS=7625
bl=69 pos[1]=[-2.1 -5.3 0.6] dr=0.78 t=99.0ps kin=5.80 pot=4.54 Rg=0.683 SPS=8434
bl=70 pos[1]=[-3.3 -4.9 0.5] dr=0.82 t=100.0ps kin=6.19 pot=4.70 Rg=0.679 SPS=8482
bl=71 pos[1]=[-3.9 -4.5 0.2] dr=1.02 t=101.0ps kin=6.62 pot=4.68 Rg=0.565 SPS=8872
bl=72 pos[1]=[-4.3 -5.5 0.5] dr=1.14 t=102.0ps kin=7.04 pot=5.07 Rg=0.536 SPS=8607
bl=73 pos[1]=[-5.0 -4.5 0.5] dr=0.87 t=103.0ps kin=5.33 pot=5.05 Rg=0.554 SPS=8651
bl=74 pos[1]=[-5.3 -3.9 0.4] dr=0.88 t=104.0ps kin=4.96 pot=5.19 Rg=0.664 SPS=8740
bl=75 pos[1]=[-6.1 -3.7 0.1] dr=1.09 t=105.0ps kin=5.61 pot=5.87 Rg=0.775 SPS=8770
bl=76 pos[1]=[-6.3 -4.0 -0.1] dr=0.69 t=106.0ps kin=5.13 pot=6.20 Rg=0.804 SPS=8922
bl=77 pos[1]=[-6.1 -3.8 -0.6] dr=0.50 t=107.0ps kin=6.57 pot=6.13 Rg=0.596 SPS=8360
bl=78 pos[1]=[-6.3 -3.9 -1.4] dr=0.57 t=108.0ps kin=5.46 pot=6.38 Rg=0.440 SPS=8492
bl=79 pos[1]=[-6.9 -3.7 -1.6] dr=0.67 t=109.0ps kin=6.07 pot=6.93 Rg=0.430 SPS=8567
bl=80 pos[1]=[-7.3 -3.6 -2.7] dr=0.86 t=110.0ps kin=4.86 pot=6.89 Rg=0.531 SPS=8621
bl=81 pos[1]=[-7.3 -3.1 -2.9] dr=0.82 t=111.0ps kin=5.23 pot=7.06 Rg=0.498 SPS=8702
bl=82 pos[1]=[-7.0 -2.7 -3.2] dr=0.55 t=112.0ps kin=6.05 pot=7.02 Rg=0.477 SPS=8684
bl=83 pos[1]=[-6.8 -2.4 -2.9] dr=0.49 t=113.0ps kin=4.13 pot=6.67 Rg=0.406 SPS=8754
bl=84 pos[1]=[-7.9 -2.5 -3.4] dr=0.86 t=114.0ps kin=4.23 pot=7.06 Rg=0.410 SPS=8740
bl=85 pos[1]=[-7.9 -2.3 -3.3] dr=0.63 t=115.0ps kin=3.89 pot=7.38 Rg=0.496 SPS=8701
bl=86 pos[1]=[-8.0 -2.4 -3.2] dr=0.59 t=116.0ps kin=2.92 pot=7.54 Rg=0.611 SPS=8898
bl=87 pos[1]=[-8.0 -2.2 -3.4] dr=0.45 t=117.0ps kin=3.57 pot=7.70 Rg=0.791 SPS=8651
bl=88 pos[1]=[-8.5 -1.9 -2.6] dr=1.04 t=118.0ps kin=4.14 pot=8.09 Rg=0.879 SPS=8940
bl=89 pos[1]=[-9.2 -1.7 -3.1] dr=0.72 t=119.0ps kin=3.87 pot=8.01 Rg=0.643 SPS=9065
bl=90 pos[1]=[-9.6 -2.0 -3.3] dr=0.77 t=120.0ps kin=3.71 pot=8.50 Rg=0.759 SPS=8609
bl=91 pos[1]=[-9.9 -1.9 -2.7] dr=0.48 t=121.0ps kin=3.23 pot=8.31 Rg=0.616 SPS=8953
bl=92 pos[1]=[-10.3 -2.2 -3.6] dr=0.62 t=122.0ps kin=2.60 pot=8.64 Rg=0.559 SPS=8671
bl=93 pos[1]=[-10.5 -1.8 -3.0] dr=0.77 t=123.0ps kin=2.44 pot=8.60 Rg=0.711 SPS=8954
bl=94 pos[1]=[-10.8 -2.5 -2.9] dr=0.61 t=124.0ps kin=2.79 pot=8.43 Rg=0.412 SPS=8637
bl=95 pos[1]=[-10.7 -2.4 -2.6] dr=0.65 t=125.0ps kin=3.95 pot=8.89 Rg=0.578 SPS=8778
bl=96 pos[1]=[-10.7 -2.6 -3.5] dr=0.57 t=126.0ps kin=5.02 pot=9.36 Rg=0.823 SPS=8796
bl=97 pos[1]=[-10.8 -2.5 -2.2] dr=0.62 t=127.0ps kin=5.71 pot=9.22 Rg=0.897 SPS=8014
bl=98 pos[1]=[-10.5 -3.7 -2.3] dr=0.89 t=128.0ps kin=6.99 pot=9.75 Rg=1.023 SPS=7503
bl=99 pos[1]=[-11.3 -3.8 -2.8] dr=0.70 t=129.0ps kin=5.48 pot=9.72 Rg=0.653 SPS=7842
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [-11.6693655 -3.76013415 -3.52913654] Rg = 0.65312004
median bond size is 0.2290878636694177
three shortest/longest (<10)/ bonds are [0.07835139 0.17617395 0.20731799] [0.31495102 0.38001044 0.68796864]
95 percentile of distance to center is: 0.8599407829757514
density of closest 95% monomers is: 3.5663943079826224
density of the core monomers is: 1.6180429828063354
min/median/mean/max coordinates are:
x: -12.33, -11.57, -11.67, -11.15
y: -3.94, -3.75, -3.76, -3.53
z: -3.99, -3.67, -3.53, -2.77
Statistics for velocities:
mean kinetic energy is: 5.478428732511492 should be: 1.5
fastest particles are (in kT): [ 4.88943464 5.23413138 6.02967511 11.86918393 14.250708 ]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 9.717581176757813
bl=100 pos[1]=[-11.6 -4.6 -2.7] dr=0.60 t=130.0ps kin=3.82 pot=10.00 Rg=0.693 SPS=8439
bl=101 pos[1]=[-11.7 -5.1 -2.5] dr=0.44 t=131.0ps kin=4.13 pot=10.19 Rg=0.795 SPS=8077
bl=102 pos[1]=[-11.5 -5.0 -2.8] dr=0.42 t=132.0ps kin=2.87 pot=10.05 Rg=0.748 SPS=7472
bl=103 pos[1]=[-11.3 -5.6 -3.8] dr=0.90 t=133.0ps kin=3.36 pot=10.43 Rg=0.795 SPS=7968
bl=104 pos[1]=[-11.4 -5.9 -3.8] dr=0.91 t=134.0ps kin=4.55 pot=10.78 Rg=0.522 SPS=7897
bl=105 pos[1]=[-11.4 -6.0 -3.8] dr=0.60 t=135.0ps kin=4.94 pot=10.77 Rg=0.399 SPS=7570
bl=106 pos[1]=[-11.7 -6.0 -4.0] dr=0.46 t=136.0ps kin=4.36 pot=10.88 Rg=0.310 SPS=8529
bl=107 pos[1]=[-11.8 -6.9 -4.3] dr=0.59 t=137.0ps kin=3.28 pot=11.15 Rg=0.455 SPS=8108
bl=108 pos[1]=[-11.7 -6.5 -4.5] dr=0.68 t=138.0ps kin=3.91 pot=11.31 Rg=0.404 SPS=8000
bl=109 pos[1]=[-12.1 -6.2 -4.2] dr=0.53 t=139.0ps kin=4.17 pot=11.15 Rg=0.630 SPS=8304
bl=110 pos[1]=[-12.4 -5.9 -5.1] dr=0.74 t=140.0ps kin=3.52 pot=11.25 Rg=0.831 SPS=8538
bl=111 pos[1]=[-12.2 -5.9 -5.2] dr=0.49 t=141.0ps kin=3.73 pot=11.25 Rg=0.843 SPS=8934
bl=112 pos[1]=[-12.3 -6.1 -4.3] dr=0.72 t=142.0ps kin=4.50 pot=10.93 Rg=0.905 SPS=8728
bl=113 pos[1]=[-12.3 -5.9 -5.5] dr=0.65 t=143.0ps kin=4.42 pot=11.36 Rg=1.113 SPS=8992
bl=114 pos[1]=[-11.7 -5.9 -5.3] dr=0.66 t=144.0ps kin=4.18 pot=11.36 Rg=0.980 SPS=8477
bl=115 pos[1]=[-11.5 -6.2 -5.3] dr=0.80 t=145.0ps kin=2.82 pot=11.73 Rg=1.060 SPS=8981
bl=116 pos[1]=[-10.3 -6.3 -5.7] dr=0.89 t=146.0ps kin=3.26 pot=11.29 Rg=0.684 SPS=8707
bl=117 pos[1]=[-10.6 -5.9 -4.4] dr=0.68 t=147.0ps kin=3.10 pot=11.00 Rg=0.614 SPS=8831
bl=118 pos[1]=[-10.9 -5.9 -4.4] dr=0.40 t=148.0ps kin=3.62 pot=11.28 Rg=0.844 SPS=8766
bl=119 pos[1]=[-11.0 -6.4 -5.0] dr=0.59 t=149.0ps kin=3.65 pot=11.41 Rg=0.864 SPS=8820
bl=120 pos[1]=[-11.4 -6.6 -5.3] dr=0.49 t=150.0ps kin=2.91 pot=11.55 Rg=0.913 SPS=8686
bl=121 pos[1]=[-10.5 -7.0 -5.5] dr=0.61 t=151.0ps kin=4.16 pot=11.48 Rg=0.846 SPS=8920
bl=122 pos[1]=[-10.2 -7.0 -5.5] dr=0.51 t=152.0ps kin=4.40 pot=11.18 Rg=0.784 SPS=8871
bl=123 pos[1]=[-9.8 -7.5 -6.1] dr=0.64 t=153.0ps kin=3.56 pot=11.34 Rg=0.884 SPS=8884
bl=124 pos[1]=[-9.0 -8.4 -5.5] dr=0.86 t=154.0ps kin=2.88 pot=11.30 Rg=0.752 SPS=8785
bl=125 pos[1]=[-8.7 -8.7 -5.1] dr=0.66 t=155.0ps kin=3.90 pot=11.31 Rg=0.687 SPS=8489
bl=126 pos[1]=[-8.8 -8.7 -5.4] dr=0.59 t=156.0ps kin=2.77 pot=11.24 Rg=0.766 SPS=8581
bl=127 pos[1]=[-8.9 -8.9 -4.9] dr=0.37 t=157.0ps kin=2.21 pot=11.23 Rg=0.772 SPS=8646
bl=128 pos[1]=[-8.2 -8.4 -4.7] dr=0.60 t=158.0ps kin=3.57 pot=10.79 Rg=0.778 SPS=8665
bl=129 pos[1]=[-8.3 -8.0 -5.1] dr=0.53 t=159.0ps kin=2.58 pot=10.93 Rg=0.554 SPS=8865
bl=130 pos[1]=[-9.4 -7.5 -5.3] dr=0.82 t=160.0ps kin=3.39 pot=10.67 Rg=0.616 SPS=8685
bl=131 pos[1]=[-9.2 -7.7 -4.6] dr=0.68 t=161.0ps kin=4.05 pot=10.29 Rg=0.789 SPS=8779
bl=132 pos[1]=[-8.2 -8.0 -4.7] dr=0.76 t=162.0ps kin=3.43 pot=10.28 Rg=0.833 SPS=9041
bl=133 pos[1]=[-8.1 -7.8 -5.0] dr=0.62 t=163.0ps kin=3.67 pot=9.90 Rg=0.847 SPS=8675
bl=134 pos[1]=[-7.7 -8.0 -4.5] dr=0.74 t=164.0ps kin=3.16 pot=9.67 Rg=1.020 SPS=8687
bl=135 pos[1]=[-7.8 -7.6 -4.0] dr=0.46 t=165.0ps kin=3.25 pot=9.66 Rg=0.798 SPS=8760
bl=136 pos[1]=[-7.9 -7.0 -4.7] dr=0.72 t=166.0ps kin=4.77 pot=9.73 Rg=0.559 SPS=8771
bl=137 pos[1]=[-7.5 -6.7 -5.0] dr=0.65 t=167.0ps kin=3.90 pot=9.72 Rg=0.618 SPS=8176
bl=138 pos[1]=[-7.8 -7.1 -6.0] dr=0.62 t=168.0ps kin=3.33 pot=10.09 Rg=0.749 SPS=7768
bl=139 pos[1]=[-6.8 -7.0 -5.3] dr=0.73 t=169.0ps kin=3.33 pot=9.77 Rg=0.824 SPS=8358
bl=140 pos[1]=[-6.6 -7.0 -5.3] dr=0.86 t=170.0ps kin=3.05 pot=9.62 Rg=0.623 SPS=8412
bl=141 pos[1]=[-6.2 -6.9 -4.7] dr=0.62 t=171.0ps kin=4.91 pot=9.59 Rg=0.788 SPS=8749
bl=142 pos[1]=[-6.2 -6.8 -4.9] dr=0.55 t=172.0ps kin=4.14 pot=9.42 Rg=0.687 SPS=8627
bl=143 pos[1]=[-6.4 -7.8 -5.4] dr=0.78 t=173.0ps kin=3.52 pot=9.99 Rg=0.741 SPS=8807
bl=144 pos[1]=[-7.3 -8.1 -5.4] dr=0.62 t=174.0ps kin=3.58 pot=9.87 Rg=0.710 SPS=8736
bl=145 pos[1]=[-6.9 -7.7 -5.9] dr=0.75 t=175.0ps kin=3.66 pot=10.24 Rg=0.651 SPS=8913
bl=146 pos[1]=[-6.9 -7.7 -5.9] dr=0.62 t=176.0ps kin=3.75 pot=10.44 Rg=0.496 SPS=8652
bl=147 pos[1]=[-7.0 -8.1 -6.1] dr=0.56 t=177.0ps kin=3.70 pot=10.53 Rg=0.386 SPS=8847
bl=148 pos[1]=[-6.9 -8.3 -6.6] dr=0.63 t=178.0ps kin=3.98 pot=10.68 Rg=0.487 SPS=8808
bl=149 pos[1]=[-6.9 -8.0 -6.6] dr=0.60 t=179.0ps kin=2.48 pot=10.69 Rg=0.427 SPS=8774
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [-6.82088323 -7.50743847 -6.68795452] Rg = 0.4274377
median bond size is 0.2728078873850459
three shortest/longest (<10)/ bonds are [0.11215107 0.1341288 0.20583282] [0.3524502 0.36537533 0.4069931 ]
95 percentile of distance to center is: 0.5868341187853655
density of closest 95% monomers is: 11.222482273223775
density of the core monomers is: 19.40923865788274
min/median/mean/max coordinates are:
x: -7.13, -6.85, -6.82, -6.54
y: -8.08, -7.35, -7.51, -7.10
z: -7.01, -6.63, -6.69, -6.41
Statistics for velocities:
mean kinetic energy is: 2.483699793026253 should be: 1.5
fastest particles are (in kT): [2.04613018 3.49250093 4.2438562 4.56766627 5.57791057]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 10.687487792968751
bl=150 pos[1]=[-7.4 -8.3 -6.7] dr=0.54 t=180.0ps kin=2.55 pot=11.11 Rg=0.413 SPS=9017
bl=151 pos[1]=[-6.7 -7.6 -6.9] dr=0.58 t=181.0ps kin=2.92 pot=10.95 Rg=0.400 SPS=8790
bl=152 pos[1]=[-6.4 -7.9 -7.0] dr=0.52 t=182.0ps kin=4.86 pot=11.09 Rg=0.526 SPS=8676
bl=153 pos[1]=[-6.9 -7.6 -7.1] dr=0.82 t=183.0ps kin=3.33 pot=11.18 Rg=0.446 SPS=8637
bl=154 pos[1]=[-8.1 -7.5 -6.9] dr=0.90 t=184.0ps kin=3.70 pot=11.44 Rg=0.654 SPS=8592
bl=155 pos[1]=[-8.0 -7.6 -6.9] dr=0.57 t=185.0ps kin=4.94 pot=11.50 Rg=0.555 SPS=8735
bl=156 pos[1]=[-8.7 -7.1 -7.2] dr=0.66 t=186.0ps kin=4.42 pot=11.65 Rg=0.597 SPS=8932
bl=157 pos[1]=[-9.0 -7.0 -7.4] dr=0.74 t=187.0ps kin=3.29 pot=12.21 Rg=0.753 SPS=8720
bl=158 pos[1]=[-9.1 -6.8 -7.6] dr=0.47 t=188.0ps kin=3.36 pot=12.14 Rg=0.632 SPS=8936
bl=159 pos[1]=[-9.4 -7.4 -7.9] dr=0.56 t=189.0ps kin=4.86 pot=12.32 Rg=0.568 SPS=7975
bl=160 pos[1]=[-9.7 -7.0 -7.9] dr=0.81 t=190.0ps kin=4.27 pot=12.75 Rg=0.708 SPS=8499
bl=161 pos[1]=[-9.3 -7.3 -8.6] dr=0.62 t=191.0ps kin=4.43 pot=12.97 Rg=0.632 SPS=8702
bl=162 pos[1]=[-10.1 -7.6 -9.1] dr=0.61 t=192.0ps kin=4.43 pot=13.01 Rg=0.854 SPS=8941
bl=163 pos[1]=[-10.5 -8.1 -9.6] dr=0.90 t=193.0ps kin=4.03 pot=13.50 Rg=1.490 SPS=8691
bl=164 pos[1]=[-10.4 -7.7 -9.9] dr=0.60 t=194.0ps kin=5.04 pot=13.00 Rg=1.358 SPS=8793
bl=165 pos[1]=[-10.0 -6.8 -10.2] dr=0.80 t=195.0ps kin=4.96 pot=13.03 Rg=1.081 SPS=8873
bl=166 pos[1]=[-9.7 -6.8 -9.5] dr=0.49 t=196.0ps kin=5.06 pot=12.85 Rg=0.978 SPS=8703
bl=167 pos[1]=[-9.5 -7.0 -9.7] dr=0.63 t=197.0ps kin=4.54 pot=12.63 Rg=0.911 SPS=9041
bl=168 pos[1]=[-9.4 -7.0 -9.3] dr=0.70 t=198.0ps kin=4.33 pot=12.87 Rg=1.272 SPS=8666
bl=169 pos[1]=[-8.8 -6.3 -8.9] dr=0.64 t=199.0ps kin=4.69 pot=12.54 Rg=1.156 SPS=8783
bl=170 pos[1]=[-8.2 -6.7 -9.3] dr=0.50 t=200.0ps kin=3.92 pot=12.40 Rg=1.083 SPS=8960
bl=171 pos[1]=[-7.8 -6.5 -9.6] dr=0.83 t=201.0ps kin=3.11 pot=12.07 Rg=0.847 SPS=9090
bl=172 pos[1]=[-7.3 -6.3 -10.1] dr=0.69 t=202.0ps kin=4.05 pot=11.83 Rg=0.547 SPS=9007
bl=173 pos[1]=[-7.0 -5.2 -9.6] dr=0.95 t=203.0ps kin=3.52 pot=11.06 Rg=0.643 SPS=8860
bl=174 pos[1]=[-6.7 -4.9 -9.4] dr=0.54 t=204.0ps kin=4.55 pot=10.90 Rg=0.730 SPS=8716
bl=175 pos[1]=[-6.4 -5.0 -9.6] dr=0.68 t=205.0ps kin=3.58 pot=10.52 Rg=0.687 SPS=8770
bl=176 pos[1]=[-6.4 -4.9 -9.7] dr=0.77 t=206.0ps kin=4.89 pot=10.17 Rg=0.791 SPS=8478
bl=177 pos[1]=[-6.5 -4.3 -10.5] dr=0.66 t=207.0ps kin=6.39 pot=10.41 Rg=0.820 SPS=7717
bl=178 pos[1]=[-6.3 -4.7 -10.8] dr=0.69 t=208.0ps kin=5.16 pot=10.58 Rg=0.795 SPS=7589
bl=179 pos[1]=[-7.2 -5.1 -10.8] dr=0.79 t=209.0ps kin=4.82 pot=11.12 Rg=0.994 SPS=8405
bl=180 pos[1]=[-7.5 -5.2 -10.9] dr=0.50 t=210.0ps kin=5.86 pot=11.17 Rg=0.903 SPS=8493
bl=181 pos[1]=[-7.2 -5.4 -10.7] dr=0.69 t=211.0ps kin=6.43 pot=11.17 Rg=1.130 SPS=8970
bl=182 pos[1]=[-7.0 -5.3 -10.7] dr=0.52 t=212.0ps kin=5.85 pot=11.27 Rg=0.939 SPS=8771
bl=183 pos[1]=[-7.3 -5.7 -10.8] dr=0.73 t=213.0ps kin=3.85 pot=11.40 Rg=1.003 SPS=8741
bl=184 pos[1]=[-7.5 -5.4 -10.9] dr=0.88 t=214.0ps kin=3.51 pot=11.40 Rg=1.045 SPS=8750
bl=185 pos[1]=[-6.5 -5.3 -11.4] dr=0.70 t=215.0ps kin=4.05 pot=11.25 Rg=0.668 SPS=8777
bl=186 pos[1]=[-6.3 -5.0 -11.4] dr=0.48 t=216.0ps kin=2.97 pot=11.01 Rg=0.587 SPS=9078
bl=187 pos[1]=[-6.3 -4.1 -11.4] dr=0.69 t=217.0ps kin=4.14 pot=11.10 Rg=0.412 SPS=8699
bl=188 pos[1]=[-5.8 -3.9 -11.0] dr=0.55 t=218.0ps kin=4.36 pot=11.16 Rg=0.529 SPS=9099
bl=189 pos[1]=[-6.1 -4.2 -11.4] dr=0.75 t=219.0ps kin=5.34 pot=11.70 Rg=0.547 SPS=8713
bl=190 pos[1]=[-6.4 -5.1 -10.9] dr=0.77 t=220.0ps kin=4.45 pot=11.69 Rg=0.904 SPS=8757
bl=191 pos[1]=[-7.1 -4.5 -10.7] dr=0.55 t=221.0ps kin=4.01 pot=11.57 Rg=0.762 SPS=8964
bl=192 pos[1]=[-7.4 -4.9 -10.3] dr=0.59 t=222.0ps kin=4.21 pot=11.54 Rg=0.890 SPS=8456
bl=193 pos[1]=[-7.8 -4.7 -9.8] dr=0.49 t=223.0ps kin=3.76 pot=11.92 Rg=0.956 SPS=8736
bl=194 pos[1]=[-7.6 -5.2 -9.8] dr=0.61 t=224.0ps kin=3.36 pot=12.00 Rg=0.958 SPS=8698
bl=195 pos[1]=[-7.2 -4.7 -9.5] dr=0.53 t=225.0ps kin=3.35 pot=11.68 Rg=0.895 SPS=8780
bl=196 pos[1]=[-7.6 -4.6 -9.0] dr=0.64 t=226.0ps kin=3.40 pot=11.49 Rg=0.915 SPS=8714
bl=197 pos[1]=[-7.6 -5.0 -9.4] dr=0.72 t=227.0ps kin=2.65 pot=11.21 Rg=0.733 SPS=8862
bl=198 pos[1]=[-7.8 -4.5 -9.6] dr=0.45 t=228.0ps kin=3.44 pot=11.27 Rg=0.597 SPS=8672
bl=199 pos[1]=[-7.7 -4.4 -9.7] dr=0.74 t=229.0ps kin=4.96 pot=11.50 Rg=0.637 SPS=8774
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [-8.5616169 -4.05691307 -9.71910019] Rg = 0.6367024
median bond size is 0.3957872159944983
three shortest/longest (<10)/ bonds are [0.21130998 0.21727112 0.29695257] [0.40486586 0.42093309 0.58961049]
95 percentile of distance to center is: 0.9417336909333655
density of closest 95% monomers is: 2.715505411951045
density of the core monomers is: 4.113783843695203
min/median/mean/max coordinates are:
x: -9.10, -8.70, -8.56, -7.66
y: -4.71, -4.07, -4.06, -3.62
z: -10.30, -9.70, -9.72, -9.36
Statistics for velocities:
mean kinetic energy is: 4.959772554216446 should be: 1.5
fastest particles are (in kT): [4.86005697 4.97256635 6.36384215 6.9767307 8.77262691]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 11.497875213623047
bl=200 pos[1]=[-8.0 -4.5 -8.9] dr=0.56 t=230.0ps kin=6.56 pot=11.59 Rg=0.793 SPS=8716
bl=201 pos[1]=[-8.5 -5.0 -9.1] dr=0.77 t=231.0ps kin=5.89 pot=11.87 Rg=1.020 SPS=8960
bl=202 pos[1]=[-8.4 -5.5 -8.4] dr=0.63 t=232.0ps kin=6.09 pot=11.51 Rg=1.127 SPS=8577
bl=203 pos[1]=[-9.0 -5.4 -7.7] dr=0.76 t=233.0ps kin=5.01 pot=11.61 Rg=1.087 SPS=7812
bl=204 pos[1]=[-8.7 -4.7 -7.5] dr=0.71 t=234.0ps kin=4.60 pot=11.38 Rg=0.907 SPS=7845
bl=205 pos[1]=[-9.0 -5.0 -7.2] dr=0.59 t=235.0ps kin=3.77 pot=11.54 Rg=1.157 SPS=8219
bl=206 pos[1]=[-9.7 -5.5 -7.8] dr=0.72 t=236.0ps kin=3.41 pot=11.82 Rg=1.087 SPS=8531
bl=207 pos[1]=[-10.2 -5.5 -7.6] dr=0.60 t=237.0ps kin=3.81 pot=11.76 Rg=0.820 SPS=8783
bl=208 pos[1]=[-10.1 -5.6 -7.0] dr=0.62 t=238.0ps kin=3.53 pot=11.95 Rg=0.825 SPS=8750
bl=209 pos[1]=[-10.5 -5.2 -7.0] dr=0.61 t=239.0ps kin=3.77 pot=11.84 Rg=0.677 SPS=8676
bl=210 pos[1]=[-10.4 -6.0 -6.9] dr=1.02 t=240.0ps kin=3.34 pot=12.22 Rg=0.803 SPS=8616
bl=211 pos[1]=[-10.0 -6.1 -7.2] dr=0.62 t=241.0ps kin=3.27 pot=12.29 Rg=0.825 SPS=8743
bl=212 pos[1]=[-9.9 -5.9 -7.4] dr=0.46 t=242.0ps kin=2.92 pot=12.35 Rg=0.888 SPS=8891
bl=213 pos[1]=[-10.1 -6.7 -7.2] dr=0.72 t=243.0ps kin=5.24 pot=12.51 Rg=0.832 SPS=8732
bl=214 pos[1]=[-10.8 -6.1 -6.6] dr=0.94 t=244.0ps kin=6.76 pot=12.74 Rg=0.649 SPS=8777
bl=215 pos[1]=[-11.7 -5.7 -7.0] dr=0.72 t=245.0ps kin=5.25 pot=12.56 Rg=0.457 SPS=8762
bl=216 pos[1]=[-12.0 -5.7 -6.4] dr=0.66 t=246.0ps kin=3.63 pot=12.42 Rg=0.261 SPS=8696
bl=217 pos[1]=[-11.6 -5.3 -6.0] dr=0.56 t=247.0ps kin=4.13 pot=12.36 Rg=0.573 SPS=8452
bl=218 pos[1]=[-11.6 -5.9 -6.5] dr=0.65 t=248.0ps kin=3.55 pot=12.35 Rg=0.395 SPS=8338
bl=219 pos[1]=[-11.1 -6.6 -6.0] dr=0.69 t=249.0ps kin=2.88 pot=12.66 Rg=0.606 SPS=8862
bl=220 pos[1]=[-10.6 -6.0 -6.3] dr=0.82 t=250.0ps kin=3.00 pot=12.81 Rg=0.765 SPS=8700
bl=221 pos[1]=[-11.2 -5.1 -7.0] dr=0.75 t=251.0ps kin=3.74 pot=13.09 Rg=0.992 SPS=8627
bl=222 pos[1]=[-11.1 -5.2 -7.0] dr=0.54 t=252.0ps kin=2.93 pot=12.97 Rg=0.862 SPS=8884
bl=223 pos[1]=[-12.2 -5.4 -7.0] dr=0.78 t=253.0ps kin=3.82 pot=13.17 Rg=0.593 SPS=8780
bl=224 pos[1]=[-12.1 -6.0 -7.4] dr=0.63 t=254.0ps kin=4.10 pot=13.17 Rg=0.448 SPS=8754
bl=225 pos[1]=[-11.8 -6.3 -7.7] dr=0.66 t=255.0ps kin=3.45 pot=13.21 Rg=0.402 SPS=8817
bl=226 pos[1]=[-12.4 -6.0 -7.9] dr=0.51 t=256.0ps kin=3.43 pot=13.33 Rg=0.429 SPS=8640
bl=227 pos[1]=[-11.7 -6.2 -7.9] dr=0.88 t=257.0ps kin=3.47 pot=12.76 Rg=0.506 SPS=9079
bl=228 pos[1]=[-11.6 -5.7 -8.1] dr=0.78 t=258.0ps kin=3.23 pot=12.53 Rg=0.697 SPS=8756
bl=229 pos[1]=[-11.6 -5.7 -9.0] dr=0.77 t=259.0ps kin=3.77 pot=12.45 Rg=0.927 SPS=8950
bl=230 pos[1]=[-11.0 -5.1 -8.3] dr=0.68 t=260.0ps kin=3.28 pot=11.90 Rg=0.672 SPS=8786
bl=231 pos[1]=[-10.6 -4.9 -8.4] dr=0.57 t=261.0ps kin=1.92 pot=11.94 Rg=0.748 SPS=8968
bl=232 pos[1]=[-9.7 -5.3 -8.7] dr=0.78 t=262.0ps kin=1.82 pot=11.72 Rg=0.490 SPS=8782
bl=233 pos[1]=[-9.3 -5.3 -9.8] dr=0.83 t=263.0ps kin=2.16 pot=11.82 Rg=0.647 SPS=8805
bl=234 pos[1]=[-9.2 -5.0 -9.0] dr=0.58 t=264.0ps kin=3.25 pot=11.55 Rg=0.442 SPS=9014
bl=235 pos[1]=[-9.5 -5.1 -10.1] dr=0.55 t=265.0ps kin=3.34 pot=11.70 Rg=0.722 SPS=8845
bl=236 pos[1]=[-8.6 -4.5 -9.7] dr=0.63 t=266.0ps kin=4.42 pot=11.32 Rg=0.646 SPS=8774
bl=237 pos[1]=[-9.3 -5.4 -9.8] dr=0.81 t=267.0ps kin=3.40 pot=11.86 Rg=0.986 SPS=9021
bl=238 pos[1]=[-9.4 -5.5 -9.8] dr=0.59 t=268.0ps kin=3.58 pot=11.83 Rg=0.834 SPS=8654
bl=239 pos[1]=[-9.7 -4.9 -9.5] dr=0.71 t=269.0ps kin=2.88 pot=11.74 Rg=0.814 SPS=8820
bl=240 pos[1]=[-9.9 -4.3 -9.3] dr=0.69 t=270.0ps kin=1.90 pot=11.69 Rg=0.440 SPS=8966
bl=241 pos[1]=[-10.3 -4.7 -9.9] dr=0.55 t=271.0ps kin=2.93 pot=12.10 Rg=0.408 SPS=8817
bl=242 pos[1]=[-10.2 -4.0 -9.2] dr=0.75 t=272.0ps kin=3.17 pot=11.97 Rg=0.503 SPS=9002
bl=243 pos[1]=[-10.1 -4.4 -9.3] dr=0.72 t=273.0ps kin=3.98 pot=11.54 Rg=0.532 SPS=8580
bl=244 pos[1]=[-10.4 -4.5 -8.5] dr=0.64 t=274.0ps kin=3.58 pot=11.80 Rg=0.390 SPS=8623
bl=245 pos[1]=[-10.4 -4.2 -9.0] dr=0.53 t=275.0ps kin=3.63 pot=11.98 Rg=0.420 SPS=7829
bl=246 pos[1]=[-10.3 -4.5 -8.6] dr=0.60 t=276.0ps kin=3.21 pot=11.83 Rg=0.406 SPS=7772
bl=247 pos[1]=[-10.2 -4.1 -8.7] dr=0.42 t=277.0ps kin=2.90 pot=11.63 Rg=0.450 SPS=8413
bl=248 pos[1]=[-11.1 -4.0 -9.1] dr=0.49 t=278.0ps kin=3.98 pot=11.63 Rg=0.511 SPS=8684
bl=249 pos[1]=[-11.0 -4.3 -7.8] dr=0.97 t=279.0ps kin=3.50 pot=11.56 Rg=0.800 SPS=8980
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [-10.4594903 -3.83772054 -8.16871872] Rg = 0.79989004
median bond size is 0.3026642386826154
three shortest/longest (<10)/ bonds are [0.13822635 0.20094276 0.27603895] [0.42819588 0.48072175 0.65386942]
95 percentile of distance to center is: 1.2738780717178375
density of closest 95% monomers is: 1.097113124705863
density of the core monomers is: 13.557885674028837
min/median/mean/max coordinates are:
x: -10.98, -10.65, -10.46, -9.64
y: -4.35, -4.00, -3.84, -3.06
z: -8.95, -8.09, -8.17, -7.61
Statistics for velocities:
mean kinetic energy is: 3.502574610084163 should be: 1.5
fastest particles are (in kT): [3.26750747 4.13017533 4.85604577 8.90375692 9.75589561]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 11.558139038085939
bl=250 pos[1]=[-10.8 -4.1 -7.3] dr=0.61 t=280.0ps kin=3.74 pot=11.34 Rg=0.516 SPS=8712
bl=251 pos[1]=[-10.5 -4.0 -7.2] dr=0.61 t=281.0ps kin=3.97 pot=11.21 Rg=0.348 SPS=8832
bl=252 pos[1]=[-10.7 -4.1 -7.7] dr=0.69 t=282.0ps kin=6.63 pot=11.55 Rg=0.524 SPS=8753
bl=253 pos[1]=[-10.3 -3.5 -7.8] dr=0.56 t=283.0ps kin=5.74 pot=11.48 Rg=0.425 SPS=9047
bl=254 pos[1]=[-10.0 -3.8 -8.2] dr=0.77 t=284.0ps kin=6.09 pot=11.08 Rg=0.345 SPS=8830
bl=255 pos[1]=[-9.6 -3.9 -8.3] dr=0.78 t=285.0ps kin=4.90 pot=10.80 Rg=0.408 SPS=8946
bl=256 pos[1]=[-9.3 -3.7 -7.7] dr=0.61 t=286.0ps kin=4.83 pot=10.55 Rg=0.488 SPS=8946
bl=257 pos[1]=[-8.5 -3.6 -7.8] dr=0.70 t=287.0ps kin=5.44 pot=10.35 Rg=0.312 SPS=8822
bl=258 pos[1]=[-8.2 -3.7 -7.7] dr=0.58 t=288.0ps kin=4.12 pot=10.20 Rg=0.350 SPS=8941
bl=259 pos[1]=[-7.8 -3.7 -7.5] dr=0.88 t=289.0ps kin=4.05 pot=10.03 Rg=0.484 SPS=8957
bl=260 pos[1]=[-7.2 -3.6 -7.0] dr=0.59 t=290.0ps kin=4.27 pot=9.77 Rg=0.623 SPS=8704
bl=261 pos[1]=[-7.8 -3.2 -7.0] dr=0.47 t=291.0ps kin=3.93 pot=9.87 Rg=0.792 SPS=9065
bl=262 pos[1]=[-8.0 -2.6 -7.2] dr=0.49 t=292.0ps kin=4.27 pot=9.77 Rg=0.893 SPS=8969
bl=263 pos[1]=[-7.9 -2.8 -7.6] dr=0.52 t=293.0ps kin=4.73 pot=9.71 Rg=0.785 SPS=8853
bl=264 pos[1]=[-7.6 -2.7 -7.5] dr=0.35 t=294.0ps kin=4.04 pot=9.46 Rg=0.636 SPS=8673
bl=265 pos[1]=[-7.0 -2.8 -7.7] dr=0.61 t=295.0ps kin=4.17 pot=9.74 Rg=0.590 SPS=8882
bl=266 pos[1]=[-7.7 -3.4 -7.7] dr=0.61 t=296.0ps kin=3.40 pot=9.71 Rg=0.822 SPS=9039
bl=267 pos[1]=[-7.6 -3.4 -8.7] dr=0.65 t=297.0ps kin=3.11 pot=9.82 Rg=0.693 SPS=8850
bl=268 pos[1]=[-7.0 -4.8 -8.9] dr=0.71 t=298.0ps kin=2.70 pot=10.19 Rg=0.789 SPS=8772
bl=269 pos[1]=[-6.8 -3.8 -9.3] dr=0.70 t=299.0ps kin=3.54 pot=10.33 Rg=0.472 SPS=8710
bl=270 pos[1]=[-6.8 -4.3 -9.6] dr=0.86 t=300.0ps kin=2.81 pot=10.69 Rg=0.731 SPS=8786
bl=271 pos[1]=[-6.8 -3.9 -10.0] dr=0.71 t=301.0ps kin=2.13 pot=10.77 Rg=0.420 SPS=8722
bl=272 pos[1]=[-7.2 -3.9 -10.4] dr=0.64 t=302.0ps kin=3.21 pot=11.05 Rg=0.664 SPS=8825
bl=273 pos[1]=[-7.9 -3.7 -10.3] dr=0.81 t=303.0ps kin=3.80 pot=10.59 Rg=0.737 SPS=8818
bl=274 pos[1]=[-7.4 -3.9 -10.2] dr=0.49 t=304.0ps kin=3.19 pot=10.65 Rg=0.921 SPS=8750
bl=275 pos[1]=[-7.2 -3.9 -10.7] dr=0.76 t=305.0ps kin=3.55 pot=10.79 Rg=0.866 SPS=8939
bl=276 pos[1]=[-7.7 -3.9 -10.9] dr=0.57 t=306.0ps kin=4.01 pot=10.87 Rg=1.187 SPS=8727
bl=277 pos[1]=[-7.9 -4.0 -11.4] dr=0.80 t=307.0ps kin=4.36 pot=11.54 Rg=1.146 SPS=8678
bl=278 pos[1]=[-7.4 -3.1 -12.3] dr=1.01 t=308.0ps kin=5.84 pot=11.41 Rg=0.683 SPS=8802
bl=279 pos[1]=[-8.0 -2.7 -13.1] dr=0.90 t=309.0ps kin=4.78 pot=11.78 Rg=0.551 SPS=8975
bl=280 pos[1]=[-7.2 -3.3 -13.4] dr=0.59 t=310.0ps kin=4.18 pot=11.71 Rg=0.582 SPS=9024
bl=281 pos[1]=[-7.5 -2.1 -13.4] dr=0.85 t=311.0ps kin=3.64 pot=11.73 Rg=0.496 SPS=8842
bl=282 pos[1]=[-7.5 -2.1 -13.7] dr=0.67 t=312.0ps kin=2.84 pot=11.95 Rg=0.519 SPS=8833
bl=283 pos[1]=[-7.8 -2.0 -14.5] dr=0.62 t=313.0ps kin=2.95 pot=12.04 Rg=0.669 SPS=8698
bl=284 pos[1]=[-7.3 -2.0 -14.8] dr=0.65 t=314.0ps kin=3.59 pot=12.41 Rg=0.704 SPS=8940
bl=285 pos[1]=[-7.1 -2.0 -14.9] dr=0.51 t=315.0ps kin=3.54 pot=12.40 Rg=0.910 SPS=8717
bl=286 pos[1]=[-8.0 -1.9 -15.1] dr=0.66 t=316.0ps kin=2.89 pot=12.35 Rg=0.870 SPS=8694
bl=287 pos[1]=[-7.1 -1.8 -15.3] dr=0.55 t=317.0ps kin=3.27 pot=12.22 Rg=0.942 SPS=8698
bl=288 pos[1]=[-6.9 -1.6 -15.1] dr=0.64 t=318.0ps kin=4.43 pot=12.27 Rg=1.023 SPS=9026
bl=289 pos[1]=[-6.8 -0.6 -15.4] dr=0.73 t=319.0ps kin=5.76 pot=12.32 Rg=0.908 SPS=8805
bl=290 pos[1]=[-7.2 -0.4 -14.9] dr=0.81 t=320.0ps kin=4.49 pot=11.94 Rg=0.482 SPS=8913
bl=291 pos[1]=[-6.8 -0.7 -15.0] dr=0.78 t=321.0ps kin=3.19 pot=11.93 Rg=0.453 SPS=8595
bl=292 pos[1]=[-7.1 -1.0 -14.8] dr=0.59 t=322.0ps kin=2.40 pot=12.10 Rg=0.465 SPS=8690
bl=293 pos[1]=[-8.0 -1.3 -14.7] dr=0.78 t=323.0ps kin=2.27 pot=12.61 Rg=0.775 SPS=8658
bl=294 pos[1]=[-7.6 -2.2 -15.2] dr=0.78 t=324.0ps kin=1.83 pot=12.92 Rg=0.608 SPS=8692
bl=295 pos[1]=[-8.1 -2.2 -15.9] dr=0.62 t=325.0ps kin=2.78 pot=13.11 Rg=0.596 SPS=8780
bl=296 pos[1]=[-8.2 -1.9 -16.2] dr=0.69 t=326.0ps kin=2.91 pot=13.65 Rg=0.678 SPS=8665
bl=297 pos[1]=[-8.4 -2.0 -16.4] dr=0.56 t=327.0ps kin=2.58 pot=13.61 Rg=0.753 SPS=8722
bl=298 pos[1]=[-7.7 -2.6 -16.6] dr=0.54 t=328.0ps kin=2.68 pot=13.57 Rg=0.716 SPS=8690
bl=299 pos[1]=[-7.8 -2.9 -17.1] dr=0.67 t=329.0ps kin=3.47 pot=13.57 Rg=0.770 SPS=8681
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [ -6.9570581 -2.07691833 -17.46098576] Rg = 0.7699985
median bond size is 0.3846091488148675
three shortest/longest (<10)/ bonds are [0.06967954 0.19571746 0.22984745] [0.42773662 0.45362855 0.65423995]
95 percentile of distance to center is: 1.1236539676747523
density of closest 95% monomers is: 1.5985904974651821
density of the core monomers is: 12.181893131569245
min/median/mean/max coordinates are:
x: -7.77, -6.86, -6.96, -6.36
y: -2.91, -2.05, -2.08, -1.47
z: -18.01, -17.47, -17.46, -16.90
Statistics for velocities:
mean kinetic energy is: 3.4704621021467426 should be: 1.5
fastest particles are (in kT): [3.06574961 4.06743248 4.39896676 6.1819497 7.19053327]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 13.570306396484376
bl=300 pos[1]=[-7.3 -2.3 -17.4] dr=0.63 t=330.0ps kin=3.88 pot=13.57 Rg=0.380 SPS=8689
bl=301 pos[1]=[-7.5 -2.5 -17.5] dr=0.57 t=331.0ps kin=3.33 pot=13.81 Rg=0.495 SPS=8201
bl=302 pos[1]=[-7.5 -2.1 -16.9] dr=0.59 t=332.0ps kin=3.46 pot=13.84 Rg=0.760 SPS=8549
bl=303 pos[1]=[-6.5 -2.5 -16.8] dr=0.66 t=333.0ps kin=2.43 pot=13.79 Rg=0.765 SPS=8913
bl=304 pos[1]=[-6.8 -1.8 -17.3] dr=0.70 t=334.0ps kin=3.78 pot=13.65 Rg=0.618 SPS=8615
bl=305 pos[1]=[-6.1 -2.6 -17.2] dr=0.73 t=335.0ps kin=3.13 pot=13.22 Rg=0.651 SPS=8659
bl=306 pos[1]=[-5.9 -1.5 -17.3] dr=0.72 t=336.0ps kin=3.37 pot=13.04 Rg=0.648 SPS=8958
bl=307 pos[1]=[-6.0 -1.9 -17.7] dr=0.71 t=337.0ps kin=3.13 pot=13.08 Rg=0.610 SPS=8667
bl=308 pos[1]=[-5.6 -2.1 -18.0] dr=0.89 t=338.0ps kin=5.31 pot=13.06 Rg=0.624 SPS=8397
bl=309 pos[1]=[-4.7 -2.1 -18.8] dr=0.93 t=339.0ps kin=4.86 pot=12.84 Rg=0.496 SPS=8928
bl=310 pos[1]=[-4.7 -2.5 -19.9] dr=0.85 t=340.0ps kin=4.09 pot=13.02 Rg=0.568 SPS=8629
bl=311 pos[1]=[-4.0 -2.6 -21.2] dr=0.86 t=341.0ps kin=4.40 pot=13.30 Rg=0.517 SPS=8782
bl=312 pos[1]=[-3.8 -1.7 -20.3] dr=0.76 t=342.0ps kin=4.30 pot=13.04 Rg=0.539 SPS=8862
bl=313 pos[1]=[-3.0 -1.2 -20.4] dr=0.89 t=343.0ps kin=4.37 pot=12.82 Rg=0.476 SPS=8989
bl=314 pos[1]=[-3.0 -0.6 -20.9] dr=0.51 t=344.0ps kin=3.88 pot=13.01 Rg=0.636 SPS=8711
bl=315 pos[1]=[-3.4 -1.0 -21.2] dr=0.62 t=345.0ps kin=3.94 pot=13.07 Rg=0.513 SPS=8890
bl=316 pos[1]=[-3.0 -0.9 -20.8] dr=0.55 t=346.0ps kin=4.44 pot=13.25 Rg=0.477 SPS=8849
bl=317 pos[1]=[-3.8 -1.3 -20.8] dr=1.05 t=347.0ps kin=4.57 pot=14.01 Rg=0.513 SPS=8756
bl=318 pos[1]=[-3.5 -1.5 -21.9] dr=0.75 t=348.0ps kin=3.83 pot=14.25 Rg=0.516 SPS=8904
bl=319 pos[1]=[-4.5 -1.5 -23.0] dr=0.75 t=349.0ps kin=2.73 pot=14.46 Rg=0.336 SPS=8768
bl=320 pos[1]=[-4.1 -1.7 -22.9] dr=0.57 t=350.0ps kin=2.76 pot=14.41 Rg=0.262 SPS=8847
bl=321 pos[1]=[-4.2 -1.7 -23.2] dr=0.53 t=351.0ps kin=3.12 pot=14.70 Rg=0.330 SPS=8987
bl=322 pos[1]=[-4.1 -1.8 -24.2] dr=0.72 t=352.0ps kin=3.50 pot=15.07 Rg=0.398 SPS=8325
bl=323 pos[1]=[-4.2 -2.7 -23.4] dr=0.69 t=353.0ps kin=2.22 pot=15.41 Rg=0.627 SPS=8682
bl=324 pos[1]=[-4.5 -2.6 -23.8] dr=0.47 t=354.0ps kin=2.45 pot=15.34 Rg=0.432 SPS=8744
bl=325 pos[1]=[-4.5 -2.1 -23.5] dr=0.60 t=355.0ps kin=2.36 pot=15.27 Rg=0.337 SPS=8620
bl=326 pos[1]=[-4.3 -2.3 -23.3] dr=0.59 t=356.0ps kin=3.01 pot=15.43 Rg=0.406 SPS=8187
bl=327 pos[1]=[-4.1 -2.6 -24.1] dr=0.88 t=357.0ps kin=3.32 pot=15.71 Rg=0.537 SPS=8506
bl=328 pos[1]=[-4.2 -2.7 -23.5] dr=0.68 t=358.0ps kin=4.05 pot=15.74 Rg=0.403 SPS=8987
bl=329 pos[1]=[-4.3 -2.8 -23.9] dr=0.59 t=359.0ps kin=3.86 pot=15.95 Rg=0.453 SPS=8908
bl=330 pos[1]=[-4.5 -2.8 -23.4] dr=0.61 t=360.0ps kin=2.93 pot=16.38 Rg=0.639 SPS=8447
bl=331 pos[1]=[-4.9 -2.1 -23.9] dr=0.99 t=361.0ps kin=4.03 pot=15.82 Rg=0.533 SPS=9007
bl=332 pos[1]=[-4.5 -2.0 -23.8] dr=0.50 t=362.0ps kin=3.41 pot=15.46 Rg=0.536 SPS=8564
bl=333 pos[1]=[-4.1 -2.1 -24.3] dr=0.51 t=363.0ps kin=2.48 pot=15.51 Rg=0.623 SPS=8895
bl=334 pos[1]=[-4.1 -1.9 -24.2] dr=0.84 t=364.0ps kin=3.05 pot=14.96 Rg=0.777 SPS=8844
bl=335 pos[1]=[-2.9 -1.6 -24.4] dr=0.76 t=365.0ps kin=3.31 pot=14.71 Rg=0.580 SPS=9045
bl=336 pos[1]=[-3.4 -1.6 -23.8] dr=0.54 t=366.0ps kin=2.28 pot=14.39 Rg=0.440 SPS=8761
bl=337 pos[1]=[-2.7 -1.4 -22.7] dr=0.76 t=367.0ps kin=2.98 pot=14.51 Rg=0.601 SPS=8865
bl=338 pos[1]=[-2.7 -1.9 -23.0] dr=0.70 t=368.0ps kin=2.88 pot=14.69 Rg=0.555 SPS=8854
bl=339 pos[1]=[-3.5 -2.0 -23.9] dr=0.62 t=369.0ps kin=2.90 pot=15.01 Rg=0.455 SPS=9010
bl=340 pos[1]=[-3.7 -2.7 -23.5] dr=0.62 t=370.0ps kin=3.87 pot=15.25 Rg=0.341 SPS=8780
bl=341 pos[1]=[-3.9 -3.5 -23.7] dr=0.54 t=371.0ps kin=5.11 pot=15.46 Rg=0.364 SPS=8835
bl=342 pos[1]=[-4.6 -2.5 -23.5] dr=0.82 t=372.0ps kin=4.99 pot=15.50 Rg=0.604 SPS=8590
bl=343 pos[1]=[-4.4 -2.7 -23.1] dr=0.49 t=373.0ps kin=3.83 pot=15.57 Rg=0.654 SPS=8972
bl=344 pos[1]=[-5.1 -2.6 -23.8] dr=0.64 t=374.0ps kin=4.36 pot=15.65 Rg=0.739 SPS=8369
bl=345 pos[1]=[-5.0 -3.0 -24.1] dr=0.64 t=375.0ps kin=4.59 pot=15.62 Rg=0.588 SPS=8883
bl=346 pos[1]=[-4.8 -2.7 -23.5] dr=0.54 t=376.0ps kin=4.04 pot=15.72 Rg=0.372 SPS=8802
bl=347 pos[1]=[-4.8 -3.0 -22.7] dr=0.85 t=377.0ps kin=4.01 pot=15.49 Rg=0.304 SPS=9060
bl=348 pos[1]=[-4.5 -2.6 -23.3] dr=0.55 t=378.0ps kin=2.24 pot=15.47 Rg=0.455 SPS=8478
bl=349 pos[1]=[-4.7 -3.0 -22.9] dr=0.75 t=379.0ps kin=3.66 pot=15.29 Rg=0.677 SPS=8877
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [ -4.74920974 -2.77802436 -22.48913288] Rg = 0.6768085
median bond size is 0.2989124361455544
three shortest/longest (<10)/ bonds are [0.19539162 0.21329073 0.21400585] [0.39466932 0.52073099 0.52660154]
95 percentile of distance to center is: 0.948579731888487
density of closest 95% monomers is: 2.6571341017828782
density of the core monomers is: 7.666077833382917
min/median/mean/max coordinates are:
x: -4.95, -4.80, -4.75, -4.45
y: -3.40, -2.90, -2.78, -1.98
z: -22.95, -22.62, -22.49, -21.77
Statistics for velocities:
mean kinetic energy is: 3.6605388313841636 should be: 1.5
fastest particles are (in kT): [3.77285172 4.5262635 5.47088405 5.69470256 7.50751067]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 15.290472412109375
bl=350 pos[1]=[-5.5 -3.0 -22.0] dr=0.95 t=380.0ps kin=4.16 pot=15.56 Rg=0.796 SPS=8983
bl=351 pos[1]=[-5.9 -3.2 -21.9] dr=0.72 t=381.0ps kin=4.50 pot=15.79 Rg=0.710 SPS=8579
bl=352 pos[1]=[-5.8 -3.2 -21.6] dr=0.67 t=382.0ps kin=3.96 pot=15.54 Rg=0.501 SPS=8945
bl=353 pos[1]=[-6.3 -3.2 -22.0] dr=0.47 t=383.0ps kin=4.33 pot=15.99 Rg=0.509 SPS=8763
bl=354 pos[1]=[-6.5 -2.1 -21.9] dr=0.82 t=384.0ps kin=4.86 pot=15.79 Rg=0.467 SPS=8856
bl=355 pos[1]=[-7.0 -2.0 -21.4] dr=0.86 t=385.0ps kin=5.59 pot=15.49 Rg=0.497 SPS=8820
bl=356 pos[1]=[-7.4 -2.8 -21.3] dr=0.52 t=386.0ps kin=4.25 pot=15.51 Rg=0.503 SPS=8062
bl=357 pos[1]=[-7.7 -2.4 -20.8] dr=0.54 t=387.0ps kin=4.38 pot=15.54 Rg=0.476 SPS=8996
bl=358 pos[1]=[-7.6 -1.8 -20.5] dr=0.65 t=388.0ps kin=3.96 pot=15.33 Rg=0.441 SPS=8985
bl=359 pos[1]=[-7.8 -1.1 -19.8] dr=0.88 t=389.0ps kin=4.36 pot=15.15 Rg=0.622 SPS=9067
bl=360 pos[1]=[-8.4 -1.2 -18.9] dr=0.97 t=390.0ps kin=4.00 pot=14.85 Rg=0.933 SPS=8504
bl=361 pos[1]=[-8.3 -0.9 -18.7] dr=0.76 t=391.0ps kin=4.37 pot=14.73 Rg=0.944 SPS=8796
bl=362 pos[1]=[-8.8 -1.4 -19.3] dr=0.64 t=392.0ps kin=3.99 pot=14.91 Rg=0.830 SPS=8940
bl=363 pos[1]=[-8.8 -0.5 -19.7] dr=0.63 t=393.0ps kin=4.02 pot=14.81 Rg=0.778 SPS=8728
bl=364 pos[1]=[-8.8 -0.4 -20.4] dr=0.48 t=394.0ps kin=3.30 pot=14.95 Rg=0.752 SPS=8854
bl=365 pos[1]=[-9.1 -0.9 -19.6] dr=0.80 t=395.0ps kin=3.00 pot=14.79 Rg=0.427 SPS=8482
bl=366 pos[1]=[-9.4 -1.1 -19.7] dr=0.43 t=396.0ps kin=3.57 pot=14.92 Rg=0.354 SPS=8819
bl=367 pos[1]=[-8.7 -0.9 -19.6] dr=0.48 t=397.0ps kin=3.37 pot=14.97 Rg=0.281 SPS=8738
bl=368 pos[1]=[-8.7 -0.7 -19.3] dr=0.46 t=398.0ps kin=3.80 pot=14.74 Rg=0.385 SPS=8935
bl=369 pos[1]=[-8.4 -1.1 -18.8] dr=0.82 t=399.0ps kin=3.08 pot=15.18 Rg=0.899 SPS=8713
bl=370 pos[1]=[-8.1 -0.5 -18.6] dr=0.76 t=400.0ps kin=4.69 pot=14.97 Rg=0.871 SPS=8899
bl=371 pos[1]=[-9.2 -0.3 -18.5] dr=0.77 t=401.0ps kin=4.40 pot=15.03 Rg=0.688 SPS=8854
bl=372 pos[1]=[-9.5 -0.4 -18.1] dr=0.69 t=402.0ps kin=5.97 pot=14.68 Rg=0.592 SPS=8528
bl=373 pos[1]=[-8.5 -0.4 -17.9] dr=0.85 t=403.0ps kin=5.22 pot=14.14 Rg=0.603 SPS=9021
bl=374 pos[1]=[-8.8 -0.8 -17.0] dr=0.68 t=404.0ps kin=6.38 pot=14.28 Rg=0.894 SPS=8848
bl=375 pos[1]=[-8.5 -0.1 -16.7] dr=0.60 t=405.0ps kin=6.40 pot=13.83 Rg=0.848 SPS=8717
bl=376 pos[1]=[-7.4 0.4 -17.0] dr=1.01 t=406.0ps kin=4.55 pot=13.21 Rg=0.619 SPS=8921
bl=377 pos[1]=[-8.4 1.0 -17.3] dr=0.65 t=407.0ps kin=4.11 pot=13.29 Rg=0.539 SPS=8211
bl=378 pos[1]=[-8.3 0.6 -17.7] dr=0.48 t=408.0ps kin=3.75 pot=13.19 Rg=0.451 SPS=8871
bl=379 pos[1]=[-8.5 0.2 -17.6] dr=0.90 t=409.0ps kin=4.80 pot=13.79 Rg=0.589 SPS=9010
bl=380 pos[1]=[-8.1 0.2 -17.7] dr=0.53 t=410.0ps kin=3.61 pot=13.66 Rg=0.801 SPS=8974
bl=381 pos[1]=[-8.6 0.6 -18.2] dr=0.60 t=411.0ps kin=4.42 pot=13.55 Rg=0.701 SPS=9023
bl=382 pos[1]=[-8.8 1.0 -17.7] dr=0.68 t=412.0ps kin=5.75 pot=13.45 Rg=0.718 SPS=8545
bl=383 pos[1]=[-8.3 1.3 -18.1] dr=0.54 t=413.0ps kin=4.45 pot=13.95 Rg=0.888 SPS=8880
bl=384 pos[1]=[-8.4 2.0 -18.1] dr=0.98 t=414.0ps kin=4.15 pot=13.83 Rg=0.949 SPS=8949
bl=385 pos[1]=[-8.5 1.9 -18.5] dr=0.50 t=415.0ps kin=3.64 pot=13.64 Rg=0.785 SPS=9044
bl=386 pos[1]=[-8.2 1.7 -17.9] dr=0.77 t=416.0ps kin=3.28 pot=13.17 Rg=0.698 SPS=8730
bl=387 pos[1]=[-8.7 1.7 -17.2] dr=0.62 t=417.0ps kin=3.61 pot=12.95 Rg=0.586 SPS=8881
bl=388 pos[1]=[-8.9 1.6 -17.5] dr=0.56 t=418.0ps kin=3.35 pot=12.85 Rg=0.409 SPS=9010
bl=389 pos[1]=[-9.3 2.6 -17.5] dr=0.72 t=419.0ps kin=3.58 pot=12.76 Rg=0.403 SPS=8401
bl=390 pos[1]=[-9.9 2.6 -16.3] dr=0.70 t=420.0ps kin=3.74 pot=12.84 Rg=0.538 SPS=8732
bl=391 pos[1]=[-9.8 1.8 -16.6] dr=0.62 t=421.0ps kin=4.33 pot=13.08 Rg=0.594 SPS=8751
bl=392 pos[1]=[-10.1 1.4 -16.3] dr=0.76 t=422.0ps kin=4.17 pot=13.37 Rg=0.718 SPS=8472
bl=393 pos[1]=[-10.3 1.8 -16.0] dr=0.69 t=423.0ps kin=2.80 pot=13.50 Rg=0.645 SPS=8995
bl=394 pos[1]=[-10.6 1.7 -16.3] dr=0.73 t=424.0ps kin=3.10 pot=13.86 Rg=0.634 SPS=8691
bl=395 pos[1]=[-10.0 1.7 -16.2] dr=0.69 t=425.0ps kin=4.02 pot=14.08 Rg=0.954 SPS=9132
bl=396 pos[1]=[-10.5 0.7 -16.7] dr=0.81 t=426.0ps kin=4.87 pot=13.47 Rg=0.391 SPS=8306
bl=397 pos[1]=[-9.5 1.2 -16.6] dr=0.70 t=427.0ps kin=6.31 pot=13.10 Rg=0.516 SPS=9112
bl=398 pos[1]=[-8.3 1.2 -17.2] dr=0.73 t=428.0ps kin=4.56 pot=13.17 Rg=0.863 SPS=8692
bl=399 pos[1]=[-8.1 -0.1 -17.3] dr=0.98 t=429.0ps kin=4.04 pot=13.49 Rg=0.816 SPS=8275
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [-9.24929199e+00 4.68029212e-03 -1.68227570e+01] Rg = 0.81600845
median bond size is 0.3156951985452715
three shortest/longest (<10)/ bonds are [0.21112407 0.22013005 0.25008355] [0.43194624 0.58942245 0.87153261]
95 percentile of distance to center is: 1.2066041299419954
density of closest 95% monomers is: 1.2910426024195374
density of the core monomers is: 3.137301104939283
min/median/mean/max coordinates are:
x: -10.28, -8.95, -9.25, -8.10
y: -0.35, -0.03, 0.00, 0.37
z: -17.27, -16.93, -16.82, -16.28
Statistics for velocities:
mean kinetic energy is: 4.0439508026924 should be: 1.5
fastest particles are (in kT): [ 3.03522292 3.23582706 6.87122308 6.87513162 12.11280547]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 13.486607360839844
bl=400 pos[1]=[-7.7 -0.7 -16.4] dr=0.87 t=430.0ps kin=3.54 pot=13.31 Rg=0.733 SPS=8689
bl=401 pos[1]=[-7.1 -0.6 -17.2] dr=0.68 t=431.0ps kin=4.00 pot=13.08 Rg=0.971 SPS=8673
bl=402 pos[1]=[-7.4 -0.9 -17.8] dr=1.01 t=432.0ps kin=3.26 pot=12.69 Rg=0.781 SPS=8663
bl=403 pos[1]=[-6.6 -0.6 -17.7] dr=0.59 t=433.0ps kin=4.09 pot=12.40 Rg=0.611 SPS=8633
bl=404 pos[1]=[-6.0 -1.1 -18.0] dr=0.78 t=434.0ps kin=4.23 pot=12.63 Rg=0.641 SPS=8824
bl=405 pos[1]=[-6.1 -1.6 -17.5] dr=0.67 t=435.0ps kin=4.02 pot=12.87 Rg=0.648 SPS=8854
bl=406 pos[1]=[-5.6 -1.1 -18.0] dr=0.57 t=436.0ps kin=3.91 pot=12.87 Rg=0.596 SPS=8606
bl=407 pos[1]=[-5.1 -1.3 -17.7] dr=0.74 t=437.0ps kin=3.35 pot=12.88 Rg=0.697 SPS=8769
bl=408 pos[1]=[-5.1 -0.9 -17.4] dr=0.54 t=438.0ps kin=2.83 pot=12.63 Rg=0.600 SPS=8807
bl=409 pos[1]=[-5.5 0.3 -17.2] dr=0.68 t=439.0ps kin=2.64 pot=12.59 Rg=0.805 SPS=8921
bl=410 pos[1]=[-5.8 -0.6 -17.1] dr=0.68 t=440.0ps kin=2.71 pot=12.34 Rg=0.636 SPS=8855
bl=411 pos[1]=[-6.2 -0.9 -17.2] dr=0.60 t=441.0ps kin=4.35 pot=12.57 Rg=0.757 SPS=8924
bl=412 pos[1]=[-5.7 -0.8 -16.8] dr=0.52 t=442.0ps kin=3.43 pot=12.23 Rg=0.736 SPS=9063
bl=413 pos[1]=[-5.1 -0.9 -17.0] dr=0.63 t=443.0ps kin=3.44 pot=12.13 Rg=0.710 SPS=8733
bl=414 pos[1]=[-4.8 -0.4 -16.4] dr=0.62 t=444.0ps kin=3.82 pot=11.75 Rg=0.674 SPS=8630
bl=415 pos[1]=[-4.8 -0.3 -16.7] dr=0.40 t=445.0ps kin=3.34 pot=11.67 Rg=0.698 SPS=9060
bl=416 pos[1]=[-5.1 0.7 -16.8] dr=0.82 t=446.0ps kin=3.79 pot=12.12 Rg=0.760 SPS=8725
bl=417 pos[1]=[-5.4 -0.3 -16.1] dr=0.88 t=447.0ps kin=3.53 pot=11.54 Rg=0.515 SPS=8995
bl=418 pos[1]=[-5.5 0.1 -16.1] dr=0.65 t=448.0ps kin=3.31 pot=11.13 Rg=0.494 SPS=8408
bl=419 pos[1]=[-6.1 0.2 -16.1] dr=0.76 t=449.0ps kin=3.43 pot=11.33 Rg=0.565 SPS=8870
bl=420 pos[1]=[-5.7 0.6 -16.1] dr=0.60 t=450.0ps kin=4.76 pot=11.11 Rg=0.428 SPS=8874
bl=421 pos[1]=[-5.6 0.7 -15.7] dr=0.61 t=451.0ps kin=3.49 pot=11.06 Rg=0.594 SPS=8892
bl=422 pos[1]=[-5.4 1.1 -15.1] dr=0.51 t=452.0ps kin=4.57 pot=10.81 Rg=0.543 SPS=8728
bl=423 pos[1]=[-5.7 0.9 -15.9] dr=0.70 t=453.0ps kin=2.60 pot=10.93 Rg=0.415 SPS=9052
bl=424 pos[1]=[-4.9 -0.2 -16.2] dr=0.71 t=454.0ps kin=3.45 pot=10.85 Rg=0.390 SPS=8810
bl=425 pos[1]=[-5.0 -0.0 -16.0] dr=0.53 t=455.0ps kin=2.29 pot=10.94 Rg=0.644 SPS=8867
bl=426 pos[1]=[-5.4 0.4 -16.4] dr=0.65 t=456.0ps kin=2.81 pot=11.19 Rg=0.611 SPS=8682
bl=427 pos[1]=[-4.7 0.7 -16.8] dr=0.52 t=457.0ps kin=4.06 pot=11.25 Rg=0.879 SPS=8668
bl=428 pos[1]=[-5.2 0.8 -16.9] dr=0.75 t=458.0ps kin=4.36 pot=11.26 Rg=0.597 SPS=9039
bl=429 pos[1]=[-5.0 0.5 -16.3] dr=0.73 t=459.0ps kin=4.27 pot=11.12 Rg=0.577 SPS=8645
bl=430 pos[1]=[-5.3 0.7 -16.4] dr=0.64 t=460.0ps kin=4.41 pot=10.87 Rg=0.424 SPS=8647
bl=431 pos[1]=[-5.2 0.5 -16.5] dr=0.54 t=461.0ps kin=2.29 pot=10.61 Rg=0.421 SPS=9061
bl=432 pos[1]=[-5.3 0.4 -16.9] dr=0.72 t=462.0ps kin=1.74 pot=10.55 Rg=0.708 SPS=8815
bl=433 pos[1]=[-5.1 0.8 -16.7] dr=0.90 t=463.0ps kin=2.84 pot=10.22 Rg=0.488 SPS=9016
bl=434 pos[1]=[-5.5 0.9 -16.7] dr=0.65 t=464.0ps kin=2.00 pot=10.46 Rg=0.537 SPS=8285
bl=435 pos[1]=[-4.4 0.6 -16.3] dr=0.85 t=465.0ps kin=2.61 pot=9.99 Rg=0.450 SPS=9021
bl=436 pos[1]=[-4.8 1.1 -16.6] dr=0.51 t=466.0ps kin=2.56 pot=9.95 Rg=0.247 SPS=8641
bl=437 pos[1]=[-5.1 1.3 -16.4] dr=0.46 t=467.0ps kin=2.13 pot=10.26 Rg=0.483 SPS=8826
bl=438 pos[1]=[-5.3 1.3 -16.2] dr=0.59 t=468.0ps kin=2.30 pot=10.46 Rg=0.702 SPS=9060
bl=439 pos[1]=[-5.1 1.3 -15.5] dr=0.81 t=469.0ps kin=3.31 pot=10.25 Rg=0.860 SPS=8042
bl=440 pos[1]=[-5.0 1.4 -15.6] dr=0.60 t=470.0ps kin=3.55 pot=9.84 Rg=0.721 SPS=8436
bl=441 pos[1]=[-4.8 2.0 -16.3] dr=0.60 t=471.0ps kin=4.48 pot=9.91 Rg=0.652 SPS=9022
bl=442 pos[1]=[-4.0 2.2 -16.3] dr=0.76 t=472.0ps kin=4.23 pot=9.87 Rg=0.595 SPS=8958
bl=443 pos[1]=[-3.0 2.0 -17.9] dr=1.01 t=473.0ps kin=3.53 pot=10.32 Rg=0.994 SPS=8784
bl=444 pos[1]=[-3.8 2.0 -17.5] dr=0.63 t=474.0ps kin=3.09 pot=10.52 Rg=0.982 SPS=8932
bl=445 pos[1]=[-3.3 1.6 -17.4] dr=0.58 t=475.0ps kin=2.87 pot=10.23 Rg=0.801 SPS=8850
bl=446 pos[1]=[-3.6 1.8 -17.7] dr=0.42 t=476.0ps kin=3.03 pot=10.26 Rg=0.699 SPS=8519
bl=447 pos[1]=[-3.2 1.6 -17.7] dr=0.63 t=477.0ps kin=2.62 pot=10.07 Rg=0.547 SPS=8831
bl=448 pos[1]=[-3.4 2.4 -17.3] dr=0.59 t=478.0ps kin=3.02 pot=9.77 Rg=0.669 SPS=9094
bl=449 pos[1]=[-3.4 1.5 -16.4] dr=0.71 t=479.0ps kin=4.42 pot=9.83 Rg=0.395 SPS=8639
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [ -3.36345565 1.21985627 -16.87211704] Rg = 0.39454287
median bond size is 0.3842564318687674
three shortest/longest (<10)/ bonds are [0.16260213 0.19316801 0.19575652] [0.43907618 0.45354976 0.57944568]
95 percentile of distance to center is: 0.5350407463409294
density of closest 95% monomers is: 14.807250524458647
density of the core monomers is: 15.212422000844722
min/median/mean/max coordinates are:
x: -3.73, -3.44, -3.36, -3.11
y: 0.97, 1.17, 1.22, 1.54
z: -17.26, -16.83, -16.87, -16.36
Statistics for velocities:
mean kinetic energy is: 4.422873201247623 should be: 1.5
fastest particles are (in kT): [4.31831137 6.61352599 6.78292078 8.14318957 9.08868905]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 9.8281982421875
bl=450 pos[1]=[-2.8 0.9 -16.7] dr=0.77 t=480.0ps kin=4.68 pot=10.10 Rg=0.424 SPS=8643
bl=451 pos[1]=[-3.4 0.7 -16.9] dr=0.63 t=481.0ps kin=5.00 pot=10.25 Rg=0.402 SPS=9143
bl=452 pos[1]=[-2.8 -0.2 -16.3] dr=0.77 t=482.0ps kin=4.15 pot=10.57 Rg=0.724 SPS=8524
bl=453 pos[1]=[-2.3 -0.6 -16.2] dr=0.63 t=483.0ps kin=5.34 pot=10.79 Rg=0.936 SPS=8974
bl=454 pos[1]=[-2.2 -0.0 -17.1] dr=0.90 t=484.0ps kin=4.55 pot=10.49 Rg=0.561 SPS=8614
bl=455 pos[1]=[-2.3 0.4 -17.8] dr=0.68 t=485.0ps kin=4.56 pot=10.41 Rg=0.392 SPS=8666
bl=456 pos[1]=[-1.8 0.4 -17.0] dr=0.83 t=486.0ps kin=5.58 pot=10.31 Rg=0.501 SPS=8850
bl=457 pos[1]=[-2.0 0.4 -17.9] dr=0.52 t=487.0ps kin=3.64 pot=10.17 Rg=0.457 SPS=9128
bl=458 pos[1]=[-2.3 0.7 -18.0] dr=0.66 t=488.0ps kin=2.96 pot=10.32 Rg=0.444 SPS=8707
bl=459 pos[1]=[-2.2 1.1 -17.6] dr=0.81 t=489.0ps kin=3.82 pot=9.58 Rg=0.548 SPS=8666
bl=460 pos[1]=[-2.5 1.0 -17.4] dr=0.46 t=490.0ps kin=3.16 pot=9.90 Rg=0.524 SPS=8799
bl=461 pos[1]=[-2.6 1.1 -16.9] dr=0.66 t=491.0ps kin=3.02 pot=9.43 Rg=0.450 SPS=8414
bl=462 pos[1]=[-3.0 1.3 -17.0] dr=0.79 t=492.0ps kin=3.72 pot=9.20 Rg=0.558 SPS=8780
bl=463 pos[1]=[-3.4 1.8 -16.4] dr=0.85 t=493.0ps kin=3.09 pot=9.52 Rg=0.537 SPS=8800
bl=464 pos[1]=[-3.4 1.8 -16.9] dr=0.49 t=494.0ps kin=2.90 pot=9.25 Rg=0.566 SPS=8799
bl=465 pos[1]=[-3.3 2.2 -15.8] dr=0.94 t=495.0ps kin=2.57 pot=9.42 Rg=0.823 SPS=8110
bl=466 pos[1]=[-3.4 2.4 -15.7] dr=0.54 t=496.0ps kin=3.58 pot=9.47 Rg=0.992 SPS=8872
bl=467 pos[1]=[-3.7 3.2 -15.8] dr=0.63 t=497.0ps kin=3.38 pot=9.32 Rg=0.970 SPS=9070
bl=468 pos[1]=[-3.4 3.3 -15.4] dr=0.72 t=498.0ps kin=3.76 pot=8.91 Rg=1.074 SPS=9097
bl=469 pos[1]=[-2.9 3.3 -15.3] dr=0.59 t=499.0ps kin=2.56 pot=8.83 Rg=1.211 SPS=8032
bl=470 pos[1]=[-2.7 2.9 -15.4] dr=0.56 t=500.0ps kin=3.02 pot=8.73 Rg=0.927 SPS=8178
bl=471 pos[1]=[-2.9 3.2 -15.3] dr=0.54 t=501.0ps kin=3.37 pot=8.59 Rg=0.997 SPS=8240
bl=472 pos[1]=[-3.3 2.0 -15.3] dr=0.78 t=502.0ps kin=4.78 pot=9.15 Rg=0.999 SPS=8574
bl=473 pos[1]=[-3.4 2.5 -15.6] dr=0.60 t=503.0ps kin=3.74 pot=9.06 Rg=0.824 SPS=9052
bl=474 pos[1]=[-3.8 2.0 -15.4] dr=0.55 t=504.0ps kin=3.82 pot=9.17 Rg=0.838 SPS=8789
bl=475 pos[1]=[-4.3 1.7 -15.5] dr=0.75 t=505.0ps kin=3.62 pot=9.58 Rg=0.682 SPS=8895
bl=476 pos[1]=[-3.7 2.6 -15.6] dr=0.73 t=506.0ps kin=4.37 pot=9.18 Rg=0.699 SPS=7879
bl=477 pos[1]=[-3.8 2.2 -16.1] dr=0.48 t=507.0ps kin=4.35 pot=9.26 Rg=0.574 SPS=8235
bl=478 pos[1]=[-4.3 2.8 -16.2] dr=0.77 t=508.0ps kin=3.21 pot=9.37 Rg=0.753 SPS=8693
bl=479 pos[1]=[-4.9 3.0 -16.4] dr=0.57 t=509.0ps kin=2.95 pot=9.09 Rg=0.716 SPS=8887
bl=480 pos[1]=[-4.6 2.8 -16.5] dr=0.59 t=510.0ps kin=3.72 pot=9.37 Rg=0.818 SPS=8602
bl=481 pos[1]=[-4.7 2.8 -16.1] dr=0.52 t=511.0ps kin=3.24 pot=8.89 Rg=0.460 SPS=9097
bl=482 pos[1]=[-3.8 3.1 -16.2] dr=0.87 t=512.0ps kin=2.98 pot=8.88 Rg=0.298 SPS=8982
bl=483 pos[1]=[-3.5 3.0 -15.6] dr=0.51 t=513.0ps kin=2.61 pot=9.01 Rg=0.478 SPS=8244
bl=484 pos[1]=[-3.1 3.3 -15.8] dr=0.57 t=514.0ps kin=2.49 pot=8.58 Rg=0.559 SPS=8796
bl=485 pos[1]=[-3.0 3.6 -15.6] dr=0.71 t=515.0ps kin=3.17 pot=8.46 Rg=0.467 SPS=8985
bl=486 pos[1]=[-3.7 3.7 -16.2] dr=0.50 t=516.0ps kin=2.78 pot=8.47 Rg=0.457 SPS=8917
bl=487 pos[1]=[-3.6 3.6 -16.3] dr=0.67 t=517.0ps kin=3.15 pot=8.49 Rg=0.536 SPS=9059
bl=488 pos[1]=[-3.5 3.1 -16.1] dr=0.68 t=518.0ps kin=4.88 pot=8.50 Rg=0.829 SPS=8624
bl=489 pos[1]=[-3.2 4.0 -15.8] dr=0.81 t=519.0ps kin=3.84 pot=8.29 Rg=0.649 SPS=7971
bl=490 pos[1]=[-3.3 4.2 -16.2] dr=0.69 t=520.0ps kin=3.76 pot=8.02 Rg=0.506 SPS=8754
bl=491 pos[1]=[-3.1 4.5 -16.6] dr=0.42 t=521.0ps kin=5.14 pot=8.14 Rg=0.504 SPS=8608
bl=492 pos[1]=[-3.4 4.9 -16.0] dr=0.59 t=522.0ps kin=4.02 pot=8.06 Rg=0.657 SPS=8906
bl=493 pos[1]=[-3.1 4.6 -16.3] dr=0.63 t=523.0ps kin=3.74 pot=8.35 Rg=0.621 SPS=8214
bl=494 pos[1]=[-2.9 4.5 -16.6] dr=0.67 t=524.0ps kin=3.34 pot=8.16 Rg=0.468 SPS=8960
bl=495 pos[1]=[-3.4 4.4 -17.6] dr=0.67 t=525.0ps kin=2.69 pot=8.10 Rg=0.491 SPS=8917
bl=496 pos[1]=[-3.0 4.7 -17.4] dr=0.61 t=526.0ps kin=3.33 pot=8.13 Rg=0.627 SPS=8328
bl=497 pos[1]=[-2.8 4.2 -17.5] dr=0.64 t=527.0ps kin=3.72 pot=8.15 Rg=0.609 SPS=9020
bl=498 pos[1]=[-3.1 3.9 -17.1] dr=0.60 t=528.0ps kin=3.24 pot=8.13 Rg=0.475 SPS=8863
bl=499 pos[1]=[-3.6 4.1 -16.4] dr=0.69 t=529.0ps kin=3.91 pot=8.12 Rg=0.795 SPS=8753
Statistics for the simulation active_Rouse_sim, number of particles: 10, number of chains: 1
Statistics for particle position
mean position is: [ -2.47716504 3.65138638 -16.65024223] Rg = 0.795313
median bond size is 0.4209681207354708
three shortest/longest (<10)/ bonds are [0.13492316 0.17139959 0.21711373] [0.51791027 0.52394512 0.54103503]
95 percentile of distance to center is: 1.1945790582981135
density of closest 95% monomers is: 1.3304247175121318
density of the core monomers is: 2.6692225971358483
min/median/mean/max coordinates are:
x: -3.63, -2.16, -2.48, -1.78
y: 2.85, 3.73, 3.65, 4.10
z: -16.91, -16.70, -16.65, -16.35
Statistics for velocities:
mean kinetic energy is: 3.914693554708942 should be: 1.5
fastest particles are (in kT): [ 2.92848127 3.30493509 3.3941556 7.45132754 13.9429566 ]
Statistics for the system:
Forces are: ['ActiveForce', 'HarmonicBond']
Number of exceptions: 9
Potential Energy Ep = 8.116238403320313
bl=500 pos[1]=[-2.8 3.9 -16.1] dr=0.49 t=530.0ps kin=3.70 pot=8.03 Rg=0.608 SPS=8727
(501, 10, 3)
Visualize trajectory¶
[7]:
#import the libraries for plotting
from matplotlib.animation import FuncAnimation
import matplotlib.pyplot as plt
# ipympl is necessary for dynamic plotting
# dynamic plotting is not supported inline
%matplotlib ipympl
fig = plt.figure(1)
ax = fig.add_axes([0,0,1,1],projection='3d')
R0=sim.N**(0.5)
ax.scatter(xyz[0,:,0],xyz[0,:,1],xyz[0,:,2],'o',color='C0')
ax.plot(xyz[0,:,0],xyz[0,:,1],xyz[0,:,2],'-',color='C0')
ax.set_zlim(-R0, R0)
ax.set_xlim(-R0, R0)
ax.set_ylim(-R0, R0)
def update(ii):
ax.cla()
p=xyz[ii]
ax.scatter(p[:,0],p[:,1],p[:,2],'o',color='C0')
ax.plot(p[:,0],p[:,1],p[:,2],'-',color='C0')
ax.set_zlim(-R0, R0)
ax.set_xlim(-R0, R0)
ax.set_ylim(-R0, R0)
anim = FuncAnimation(fig, update, frames=np.arange(1,400,1), interval=200, blit=False,repeat=False)
# uncomment below to save the animation
# anim.save('animation_active_sim.gif', writer='pillow')
plt.show()
Verify dynamics¶
[14]:
from CndbTools import cndbTools
cndbT = cndbTools()
def active_gas_MSD(t_lag, temp, F, tau, g, d=3):
return d*(2*temp*t_lag/g + (2*F**2*tau/g**2)*(t_lag + tau*np.exp(-t_lag/tau)) - 2*F**2*tau**2/g**2)
def tau_rouse(p,kb,N,g):
return g*N**2/(np.pi**2*kb*p**2)
def active_Rouse_MSD(t_lag, temp, F, tau, kb, N, g, d=3):
rouse_modes=np.arange(1, N+1, 1)
tau_mode_i=tau_rouse(rouse_modes, kb, N, g)
val=(tau_mode_i*(temp+F**2*tau*tau_mode_i**2/(g*(tau_mode_i**2-tau**2)))*(1-np.exp(-t_lag/tau_mode_i))/(2*N*g)
-(F*tau*tau_mode_i)**2*(1-np.exp(-t_lag/tau))/(2*N*g**2*(tau_mode_i**2-tau**2)))*0.5
# print(val.shape)
return (2*d*(temp+F**2*tau/g)*t_lag/(N*g) - 2*d*F**2*tau**2*(1-np.exp(-t_lag/tau))/(N*g**2) + 8*d*np.sum(val))
[15]:
# compute_MSD returns an (N * T) array with mononers in the first dimension and lag time in the second
msd_rouse = np.mean(cndbT.compute_MSD(xyz), axis=0)
[16]:
%matplotlib inline
#lag times
ts = np.arange(0,xyz.shape[0], block_size*0.001)
plt.loglog(ts, msd_rouse,'o', label='simulation')
plt.loglog(ts, [active_Rouse_MSD(xx, sim.temperature*0.008314, F, sim.integrator.corrTime, kb, sim.N, 1.0) for xx in ts],'k--', label='analytical')
plt.legend()
plt.ylabel('Mean square displacement ($\\sigma^2$)')
plt.xlabel('Lag time $t/\\tau_{sim}$')
plt.title('Temperature={0:.2f} $F={1:.1f}\\epsilon/\\sigma$ $\\tau={2:.1f} \\tau_{{sim}}$'.format(sim.temperature,F, sim.integrator.corrTime))
plt.ylim(msd_rouse[1]*0.5,max(msd_rouse)*1.5)
plt.show()
