R: [gmx-users] electrostatic forces

Gianfranco Bocchinfuso gianfranco.bocchinfuso at uniroma2.it
Fri Jan 22 09:51:27 CET 2010

Thank you for your reply,


Really, I don’t think that the difference come from the 1-4 interactions. 

I have excluded all the 1-4 interaction involving atoms in the indole group
(deleting them from the pairs list). Furthermore, I have added the indole as
an energygrps, and checking the 1-4 energy terms in this group, they are
correctly 0 both in the simulation with the charges and in the simulation
with charges=0



Da: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Per
conto di Berk Hess
Inviato: venerdì 22 gennaio 2010 9.11
A: Discussion list for GROMACS users
Oggetto: RE: [gmx-users] electrostatic forces



I guess this is caused by the 1-4 interactions.
These also contain electrostatic interactions, which are turned off when
you turn off the charges, but not by the energygrp_excl option.



From: gianfranco.bocchinfuso at uniroma2.it
To: gmx-users at gromacs.org
Date: Thu, 21 Jan 2010 18:58:14 +0100
Subject: [gmx-users] electrostatic forces



I would like to calculate the electrostatic forces on the atoms of an Indole
group (in a TRP residue). 

I have performed two reruns of my simulation with two different topologies :
a normal topology and a topology with all the Indole charges set equal to 0.
I have also added energygrp_excl = Indole Indole (to delete electrostatic
force inside the Indole) and also I have deleted in both topologies all the
pairs between atoms belonging to the Indole group (to delete the
electrostatic contribution coming from 1-4 interactions inside the Indole
group). Furthermore I have used a very simple mdp file (with cut-off,
without DispCorr etc.) to avoid contribution coming, for example, from ewald
summation. In these conditions I expected that the differences between the
forces computed in the two simulations were due only to the electrostatic
interactions with the other atoms of protein and with solvent (SPC). 

Checking the obtained forces I see that atoms of the Indole (i.e. the CD2
and CE2), with charges equal to 0 in both topologies, show different forces
in the two simulations.

What could be the origin of this difference?  



Thank you 





New Windows 7: Find the right PC for you. Learn more.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100122/b26ea629/attachment.html>

More information about the gromacs.org_gmx-users mailing list