Re: [AMBER] solvent-solute interaction energy

From: <>
Date: Wed, 9 Jun 2010 01:11:56 +0200 (MEST)

hi my dear,

i'm relatively new at all that simulatiopn stuff at all, but what about
calculating non-bonded energies (lennard jones and coulomb interactions)
between the different groups in your system, since you seem to be looking
for interaction energies. in that case you might proceed as follows:

in your mol dynamics's mdp file set the energygrps parameter for example like

energygrps = sugarResiduesName solventsResidueName ionResidueName ...

do your dynamics (md.tpr) which should generate an output file denoted as
"md.edr" (or with another name depending on the tpr file's name but with
the same file type) containing all information you will ever need. this
includes interaction energies between any pair of those groups, that
you've defined in the step before. access the file with the command

g_energy -f md.edr -o md_ergTemp

from the list choose the types of energies/quantities you're interested in
(probably something like "LJ-SR:sol-sug" and "Coul-SR:sol-sug" by typing
the number that is associated with it followed by ENTER, and the next
number, and so on and a zero in the last line. e.g.


i really hope, that was what you wanted to know.


> Dear all,
> I'm trying to do molecular dynamics of sugar solvation in ionic liquid
> I would like to obtain solvent-solute interaction energy. (interaction E =
> (Etotal) - (Esugar) - (Esolvent))
> I've got the information of total energy(Etot) from mdinfo file. But I
> don't
> know how to calculate (Esugar) and (Esolvent).
> Thank you in advance.
> Regards,
> Hoshin Kim
> ----------------------------------------------------------------------------
> -------
> Hoshin Kim
> Now)
> Visiting Scholar
> Department of Chemical and Biomolecular Engineering
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-986-9258
> Also)
> Graduate student (M.D. candidate)
> Ionic Liquids Team(ILs) in Bio Nano Process Lab
> Department of Biological Engineering,
> 2S 113, Engineering building Inha University,
> 253 Yonghyeon Dong, Nam Ku
> Incheon, KOREA
> TEL) +82-32-860-8655
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Received on Tue Jun 08 2010 - 16:30:04 PDT
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