[gmx-users] COM distances

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Jul 7 13:59:03 CEST 2010

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)?



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

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