[gmx-users] Dihedral with parameters set to zero

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 10 19:27:38 CET 2008

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 <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] Dihedral with parameters set to zero
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4785235F.2090703 at xray.bmc.uu.se>
>> 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.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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