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

[Justin A. Lemkul]

lloyd riggs wrote:
> 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> 
> Message-ID: <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,
> 
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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.
> 

You can do this to get nonbonded interaction energies between your desired 
groups and the rest of the system, but whether or not that actually corresponds 
to a "hydrogen bonding energy" is extremely debatable.  Some force fields have 
an actual component of their functional form dedicated to this quantity, so 
trying to fudge your way into recreating this is probably not possible.  Also, 
you'd probably have to do the re-runs dozens of times with hundreds of energy 
groups each time, since the maximum is 256, and even for a small system there 
are many thousands of possible hydrogen bonds.  The .edr files quickly get out 
of hand in terms of their size.

-Justin

> Grüsse
> 
> Stephan Watkins

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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