[gmx-users] Dihedral with parameters set to zero
J.J.M.vanBemmelen at student.TUDelft.NL
Thu Jan 10 20:17:21 CET 2008
Hmmm, thanks. An obvious solution, but I had not yet thought of that
Well, you know what they say:
Een dag niets geleerd is een dag niet geleefd! ;-)
>Date: Thu, 10 Jan 2008 19:27:38 +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: <4786639A.6060806 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>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?
>> 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.
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