Hi Thomas Thanks for your help
Cheers Gavin Thomas Schlesier wrote: > The force acting on your pulled group is: > F=k(vt-x) > where x is the displacment of that group (1) relativ to group (0). > I thin Justin used this values to create the structure for the later > umbrella sampling, so the pulling velocity is rather fast. > I usually used k1=500, and velocities of about 0.001 to 0.0001 for > pulling experiment for systems with only a few hydrogen bonds. > I think the choice of the parameters depends upon how strong your > molecules interact with another. > But for umbrella sampling i would assume that it matters most that you > generate strucutres with the right distance and not so much with what > pulling velocity you reached this distances. > > Greetings > Thomas > >> >> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
