Hi All I have generated a series of configurations for two molecules approaching along the z axis. I am now going to run umbrella sampling of these configurations at a fixed distance (XYZ) in order to calculate the PMF. I understand that the output of the pulling code gives a pullx.xvg file which serves as the input to g_wham. I notice that this file does not contain the distances between the COMs of the two molecules. Is there anyway of generating a file that contains such information directly form mdrun or do I have to run g_dist for every trajectory generated. If this is the case can the output from g_dist serve as the input for g_wham (like pullx.xvg).
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
