From: Jiang ran <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: <[email protected]>
Subject: [gmx-users] BUG!!!!: FENE bond stretching potential
Date: Thu, 28 Jun 2007 23:07:55 +0800
Hello people,My professor and I tried to use the FENE potentials to relax a
protein from a unstable configuration for publishing paper. However, these
potentials didn't seem to work. Checking both the manual and the code of
the GROMACS software package for moleculair dynamics we found some things
we do not understand both me as even my professor.First one thing: In file
bondfree.c in gmxlib the force constant kb (parameter: real kb) for the
FENE potential is not included anywhere in the force neither potential
calculation . bm = forceparams[type].fene.bm; kb =
forceparams[type].fene.kb; bm2 = bm*bm; omdr2obm2 = one - dr2/bm2;
vbond = -half*bm2*log(omdr2obm2); fbond =
-bm/omdr2obm2;Second one next thing:In the following lines:The scalar force
is composed over its dimension by dx[m]:fij=bond*dx[m]However in stead of
taking a unit normalized vector the original connecting vector is taken.
The manual isn't clear about this either, but looking at the equations it
doens't make a lot of sense to me and my professor to use the original
connecting vector.Greetings from China,Jiang
Indeed the code is wrong (apparently nobody ever tried to use it,
including the person who coded it (myself)).
The potential and force should be multiplied with kb and bm should
not be in the force:
vbond = -half*kb*bm2*log(omdr2obm2);
fbond = -kb/omdr2obm2;
I also noticed that in the manual there is a minus sign missing
in front of the force.
Thanks for reporting this bug,
Berk.
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