Chris, > I don't know the answer to the exact question that you have posed, but > I instead suggest that getting rid of that water molecule is not a > good idea. You should rather minimize your system. While minimizing, > be sure to include > > define=-DFLEXIBLE > > in your .mdp file
Just out of curiosity, why do you think minimization should be done with flexible water? I've gone the opposite direction and only minimize with steepest descents since that's the only minimization algorithm in gromacs that will work with constraints on hbonds, which is how I run my dynamics, and I want to be minimizing on the same potential energy landscape in which I'm running dynamics. That seemed important. I'm curious why your strategy is different. Thanks, David _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
