van Bemmelen wrote:
OK. Now I'm confused. What did you mean by the second part?
Of course, when doing FEP with the B state different, you would
gradually introduce a dihedral as lambda increases. But that would still
mean that setting all dihedral parameters to 0 for the A state would be
exactly equivalent to having no dihedral at all, only for the simulation
at lambda=0.0. Right?
Or did you mean something else?
Thanks,
Jeroen
P.S. Actually, in such a setup one would probably run into trouble
anyway because according to the manual the multipliciy cannot be
perturbed. But let's ignore that for now.
but that can be solved by defining two dihedrals with different mult and
turn off one and turn on the other.
Date: Wed, 09 Jan 2008 20:41:19 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Dihedral with parameters set to zero
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
van Bemmelen wrote:
Hi guys,
Probably too simple for you guys, but I just need to be sure:
Am I right if I say that a GROMOS96 proper dihedral with all
parameters
set to 0 (done automatically by grompp) is exactly equivalent to no
proper dihedral at all, both with respect to all the energy terms and
with respect to the dynamics? Or is there some catch I
haven't thought
of?
that's correct, unless you would be doing FEP with the B state
different.
Thanks,
Jeroen
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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