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
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.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
myself.
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 <[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:
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.
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