Hi Justin Thanks for your help. The two molecules are now moving together. I am however slightly confused about the parameters pull_rate1 and pull_k1. I want the molecules to come together very slowly therefore I would set the rate to be a very small value. How the does the force come into play and how should you decide on the best value?
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Thanks. If I use the pull_geometry = direction I would go for the >> following jus t to pull the molecules together in the z direction. >> >> pull = umbrella >> pull_geometry = direction >> pull_start = yes >> pull_ngroups = 1 >> pull_group0 = cage_1 >> pull_group1 = cage_2 >> pull_vec1 = 0.0 0.0 -1.0 >> pull_rate1 = 0.01 >> pull_k1 = 1000 >> >> >> Does this seem reasonable? Also in the pull_rate what is meant by the > > Probably. Try it. > >> 'rate of change of the reference position'? (Is it the position of the >> reference group, if so what if I don't want it to change?) >> > > It is the rate of change of the reference position, which is the > position at the outset of the simulation. Your objective is to pull > your two species together, right? I don't see why you wouldn't want > it to change. You're not changing anything about pull_group0 (your > reference group), since you aren't setting pull_rate0. Everything is > applied to pull_group1 (hence _rate1, _k1, etc). > > -Justin > >> Cheers >> >> 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