Hi all Could someone please get back to me on this. I have ran two sets of umbrella sampling simulations 1- Using pull_geometry = distance, and pull_dim = Y Y Y 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125 0.735968 In both cases I wish to calculate the PMF for taking a host out of a guest. I specify the distance between the COM of the two groups in the respective mdp files. The two curves I get are completely different which has leads me to ask a couple of questions:
1) Does the vector change as the dynamics evolves (i.e is it just relative between the two points) or does it remain fixed in space? 2) Using umbrella sampling in the second case does the relative position of the pull group (guest) fluctuate about the distance along the specified vector? Note- I couldn't run g_wham with pull_geometry = direction in my current version of gromacs, so I ran it in 4.5.3 but I had to use the -if pullf-files.xvg option. Some help would be appreciated as I have to be sure of what the program is actually doing. 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/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
