[gmx-users] COM distances

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jul 7 19:06:49 CEST 2010

The pullx file should contain everything that you need. dX,dY,dZ *are*  
the components of the distances between the two groups.

I still don't understand your question (perhaps you could give us a  
worked example with real data?), but if you just want the COM  
distance, then try this:

cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}' > my.dist

of vourse, what you need depends on your pull code options, but this  
should give you a start. Combine this with VMD and you should be able  
to figure out what you need.


-- original message --

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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