Re: calculate cumulative dG

From: Brian Radak (
Date: Tue Aug 29 2017 - 10:08:25 CDT

Hi Nehad,

I think I understand your question, but I do not have substantial
experience with ParseFEP. It might be better if you posed this question
to the VMD listserv, since that is a VMD plugin.

As a guess - maybe you can just load the simulation in increments and
run separate ParseFEP calculations? I don't know if ParseFEP has
subsampling options, although that would be very useful.



On 08/29/2017 12:18 AM, Nehad Elsalamouny wrote:
> Dear namd users,
> I ran FEP calculation over 20 windows (forward and backward) for 10ns. I used parsefep (BAR) to analyse my data. I want to check the convergence. What I have from my calculation is the dG for each window (i.e. dG (1ns to 2ns, then 2ns to 3ns, and so on) so I need to calculate the cumulative binding free energy. How can I do this?
> Thanks in advance
> Nehad

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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