Hi all In hindsight I think the question I posted yesterday may have been a little naive. To rephrase it - If the pullx.xvg files contain X Y Z dX dY dZ, (because pull_dim = Y Y Y), does the g_wham programme calculate the centre of mass distances to use in the histogram i.e. Will the first column in the histo.xvg file be the centre of mass distances (the modulus of the three vector components)?
Cheers Gavin Gavin Melaugh wrote: > 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
