[gmx-users] Dihedral with parameters set to zero

van Bemmelen J.J.M.vanBemmelen at student.TUDelft.NL
Thu Jan 10 18:27:41 CET 2008

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?


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.

>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 
>> 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 
>> Thanks,
>> Jeroen

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