[gmx-users] COM distances

[Gavin Melaugh]

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