[gmx-users] short-range eletrostatic energy of every aminoacid

Ullmann, Thomas thomas.ullmann at mpibpc.mpg.de
Mon May 25 20:52:29 CEST 2015

Hi Diogo,

create an index file, either with gmx select or gmx make_ndx, and feed it to grompp.

Happy computing,

R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullmann at mpibpc.mpg.de

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Diogo Martins de Sá [sadiogo at mol.bio.br]
Sent: Monday, May 25, 2015 8:38 PM
To: gmx-users
Subject: [gmx-users] short-range eletrostatic energy of every aminoacid

Hello guys,

I'd like to do make an energy matrix of every aminoacid of a simulation
of two interacting proteins. I know enemat can assess the matrix, but
for this I have to define energygroups in .mdp files. What would be the
easiest way to achieve this?

I guess if I am going to find an easier way, I have to understand how
gromacs "finds" the energygroups I have written down in the .mdp file.
Lets say I manage to write down all the aminoacids I want in the
energygroups of the .mdp file. How would gromacs know where to look for
the atoms comprising each aminoacid? An index file, a topology file?

Thanks in advance.

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