[gmx-users] Re:Energy dur to Hydrogen Bonds

[lloyd riggs]

Message: 4
Date: Mon, 27 Dec 2010 18:53:52 +0530
From: Anirban Ghosh <reach.anirban.ghosh at gmail.com>
Subject: [gmx-users] Energy due to Hydrogen bonds
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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    <AANLkTi=JDDO4WWXOXuhtbmqcr_v80LAbQ1dujCtxmbd5 at mail.gmail.com>
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Hi ALL,

Is there any means to calculate the total energy arising due to the breaking
and formation for hydrogen bonds only in GROMACS?
Does the .edr file contains this information? If yes then how to parse it? I
don't think the .log file records this value.
Any suggestion is welcome.


Thanks,

Anirban
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Dear Anirbin,

You can also make a complicated index file for all the hydrogen bonds (ie atoms involved) before the run.  If you run the same MD from an initial point, the runs are identical, so you can do a run, id the atoms of interest, make an index file,re-run the MD and have these particular groups written to the .edr files, etc...and can then go through and look at your particular bonds formed or broken as of interest.  I would listen to justin's advice more though, as he's pure gromacs/sims and I might be slightly off in my advice.

Grüsse

Stephan Watkins
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