Thanks Justin Is it possible to use g_wham with pull_geometry = direction, I read on the website that you couldn't but was wondering if this had changed?
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi All >> >> I am using COM pulling to pull two molecules together in order to >> calculate the potential of mean force and the pulling is fine. I am >> using pull = umbrella for the pulling as I am following >> the tutorial on the website. If I use pull = constraint does this still >> pull the molecules together, and if so do you still then need to >> perform umbrella sampling on the configurations generated? I am a little >> confused as I don't understand how the molecules pull together if they >> are constrained. >> > > For plain SMD, you can use any of the pull methods. In the tutorial I > wrote, I explain why I used "pull = umbrella" during SMD. Umbrella > sampling is a separate procedure, which can be done after SMD. If you > want a free energy along the reaction coordinate, there are several > methods for doing this, among which is umbrella sampling. > > -Justin > >> Many Thanks >> >> Gavin > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
