[gmx-users] tutorial for relative free energy calculations

Asaf Farhi asaf.farhi at weizmann.ac.il
Mon Dec 16 09:36:30 CET 2013

Dear Gromacs Users

Is there a Gromacs tutorial for relative free energy calculations (solvation or binding)?

Thanks in advance,
Best regards,
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of lloyd riggs [lloyd.riggs at gmx.ch]
Sent: Monday, December 16, 2013 1:17 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Bin files of g_sham

I will attempt an answer, however there might be a better response.  It depends on your input .xvg (what the first column is) and what you are telling it to do (defualt is time), and if these correspond to your time frames (can be timepoint or siply frame # I believe).  g_sham seems (to me) to work like a comand line spread sheet manipulator with some built in functions. If you want a particular frame from a trajectory time point, then use g_traj with the first/last set to the frame you want but there's also 2 other tools that do this the same way...

Stephan Watkins
Gesendet: Sonntag, 15. Dezember 2013 um 14:49 Uhr
Von: "Ankita Naithani" <ankitanaithani at gmail.com>
An: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Betreff: [gmx-users] Bin files of g_sham

I had a query regarding the bin files generated by g_sham.
Does the bin index contain timepoints? i.e. there are 1024 bins so each bin
has a number of time points? And supposes bin 756 has numbers like 3876,
20020, 7896 so these would all correspond to time and we could then dump
the representative frame corresponding to these time points?

I am a little confused as to what is stored in the bins? Timepoints or
frame number and then alternatively how to get the representative
frame/snapshot stored at that specific bin number.

Kind regards,

Ankita Naithani
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