[gmx-users] 2D umbrella sampling simulation
unfortunately not. It will be done eventually though: to follow the progress of that feature, check out: http://redmine.gromacs.org/issues/1346 If you have to do that, there is a patch that I posted on that same redmine page (posts 8 and 9) to allow this in gromacs 4.0.5. Chris. -- original message -- Thanks for your check. Yes, it should be pull_group2 for C. In this case, the two distances have a reference group B. What about the case in which no common reference group is shared with the two distances, e.g. distance1 is defined as A-B and distance2 as C-D? Can current gromacs codes perform 2D umbrella sampling for this problem? Many thanks. Mingjun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] 2D umbrella sampling simulation
Your restraint involving group C should use pull_group2, etc, not another copy of pull_group1. Other than that, it looks like a valid approach. Chris. -- original message -- I am going to perform the two-dimensional umbrella sampling using a pair of distances (the distance btw atoms A and B, C and B) in the restraints. Could someone please tell whether I can use the current pull code as follows? - ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = no pull_ngroups= 2 pull_group0 = B pull_group1 = A ;restraint of distance btw A and B pull_init1 = 2.7 ;equilibrium distance of A-B pull_rate1 = 0.0 pull_k1 = 2000 ; kJ mol^-1 nm^-2 pull_group1 = C ;restraint of distance btw C and B pull_init1 = 3.7 ;equilibrium distance of C-B pull_rate1 = 0.0 pull_k1 = 2500 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps - Many thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
