From: Brian Radak (bradak_at_anl.gov)
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.
HTH,
Brian
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 brian.radak_at_anl.gov
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