Hmm, interesting... And what about the -DFLEXIBLE definition in your mdp file during steepest descent minimization? Do you know if that will also deform your (SPC) water molecules? And will that deformation be corrected again during the first equilibration step(s)?
I ask this, because I read on severel places (e.g. the online mdp options manual and in one of the tutorials) that you could use the - DFLEXIBLE definition to "allow steepest descent to minimize further". So I've used it for most of my minimizations up til now, assuming that was the right thing to do. Thanks, Jeroen On 17 Mar 2007 at 12:00, David Mobley wrote: > Sorry to e-mail so much. But it seems this is, indeed, the problem. > For freeze groups to work in minimization you need to use a minimizer > which is can handle constraints properly. In GROMACS the only > minimizer that is set up to handle constraints properly is steepest > descents. > > Note that this also has implications for anyone using rigid water > models (most of us): If you're "minimizing" with L-BFGS or other > minimizers aside from steepest descents, you're probably deforming > your water molecules, as well. > > David _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
