Attempted Tutorial, got: Particle coordinate is nan
Posted: Sat Feb 06, 2021 8:59 pm
Hello,
I'm trying to run the script from here:
http://openmm.org/tutorials/alchemical-free-energy/
But got "Particle coordinate is nan" while running. Do you know why? Thanks.
Here is my version. and I tested with openCL and CPU, both got the error.
openmm 7.4.1 py36_cuda101_rc_1 omnia
openmmtools 0.20.0 py36_0 omnia
Also, the energy definition:
energy_function = 'lambda*4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;'
energy_function += 'reff_sterics = sigma*(0.5*(1.0-lambda) + (r/sigma)^6)^(1/6);'
energy_function += 'sigma = 0.5*(sigma1+sigma2); epsilon = sqrt(epsilon1*epsilon2);'
seems at odd with the cited reference.
0.5*(1.0-lambda) I think should be (1.0-lambda)^2. and I don't see the point of doing x^(1/6)^6.
But this doesn't fix the problem.
I found a newer version of the same code in GitHub,
https://github.com/openmm/openmm/blob/m ... tential.py
I can run this script, by changing
from timeseries import subsampleCorrelatedData
to:
from pymbar.timeseries import subsampleCorrelatedData
The result I got is:
Free energy of inserting argon particle: 4.383 +- 0.465 kT
But I can't find a reference paper or document to confirm if this is right or wrong.
Is there a paper that has a figure on this? Thanks.
I'm trying to run the script from here:
http://openmm.org/tutorials/alchemical-free-energy/
But got "Particle coordinate is nan" while running. Do you know why? Thanks.
Here is my version. and I tested with openCL and CPU, both got the error.
openmm 7.4.1 py36_cuda101_rc_1 omnia
openmmtools 0.20.0 py36_0 omnia
Also, the energy definition:
energy_function = 'lambda*4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;'
energy_function += 'reff_sterics = sigma*(0.5*(1.0-lambda) + (r/sigma)^6)^(1/6);'
energy_function += 'sigma = 0.5*(sigma1+sigma2); epsilon = sqrt(epsilon1*epsilon2);'
seems at odd with the cited reference.
0.5*(1.0-lambda) I think should be (1.0-lambda)^2. and I don't see the point of doing x^(1/6)^6.
But this doesn't fix the problem.
I found a newer version of the same code in GitHub,
https://github.com/openmm/openmm/blob/m ... tential.py
I can run this script, by changing
from timeseries import subsampleCorrelatedData
to:
from pymbar.timeseries import subsampleCorrelatedData
The result I got is:
Free energy of inserting argon particle: 4.383 +- 0.465 kT
But I can't find a reference paper or document to confirm if this is right or wrong.
Is there a paper that has a figure on this? Thanks.