Hello everyone, I would like to clarify exactly what is restrained in a simulation when doing umbrella sampling, using "pulldim = Y Y Y" in the .ppa input file.
Consider you have the following in the .ppa file: verbose = no runtype = umbrella ngroups = 1 group_1 = B reference_group = A reftype = com reflag = 1 pulldim = Y Y Y k1 = 1000 pos1 = 1.5 2.5 7.0 The output .pdo file will give three columns of output, one for x , y and z direction. What I need clarified is whether, in a simulation demonstrated above, it is the DISTANCE of the vector between the center-of-mass of group A and B that is being restrained or the actual vector with each component being restrained itself. i.e., is the umbrella restraining force being applied on the DISTANCE or the actual vector. I found this question was asked in a previous post but was not answered. Thank you. -Dina _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
