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. >Date: Wed, 09 Jan 2008 20:41:19 +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: >> 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
