Open meghaparashar2 opened 4 days ago
Dear Megha,
This is a fair question, the workflow for this is a little complicated.
abf_integrate
will only integrate a single gradient grid, it won't integrate all the time steps stored in a history file. The good news is that history files are just concatenated grid files, so you can split the hist.grad file and process each of the fragments with abf_integrate
then concatenate the resulting free energy files.
Once you have a history file, the simplest way to look at convergence is with this script:
import colvars_grid as cvg
import matplotlib.pyplot as plt
pmf_traj = cvg.colvars_grid('mysim.hist.pmf')
plt.plot(pmf_traj.convergence())
This uses the Python module found here: https://github.com/Colvars/colvars/blob/master/colvartools/colvars_grid.py
Dear J Henin, Thanks for your quick reply. While going through the paper I noticed there are 4 convergence criterion used by the authors (Fig.5 & Fig.6). But the colvars_grid module is acting like a black box, I have no idea what is going on. I had few questions about this like:
Can you please refer me to a more explained documentation of these?
Thanks much! Megha
Dear J Henin, I think I have understood most of the part of convergence calculations. Though I have to ask one thing, what does 'nats' mean, that's you have used in the plot of sampling entropy and sampling heterogeneity?
Thank you! Megha
Dear all, I am using eABF free energy method to calculate dimerization energy. For this I have divided the 1d CV space in different windows and did the simulations. Now I am having .czar.grad files as well .hist.grad files. I used InputPrefix to get the PMF. Now to check the convergence I want to use abf_integrate but documentation is not very clear on how to use it. I had few questions about it, like:
Thanks, Megha