[gmx-users] Dihedral with parameters set to zero
mgoette at mpi-bpc.mpg.de
Fri Jan 11 11:24:46 CET 2008
No Holland-Speek here! ;)
Anyway, you maybe right...:)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
van Bemmelen wrote:
> 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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