[gmx-users] COM distances

Gavin Melaugh gmelaugh01 at qub.ac.uk
Wed Jul 7 19:12:09 CEST 2010

Hi Chris

Sorry I sent my e-mail just prior to receiving yours? Is it any clearer?

chris.neale at utoronto.ca wrote:
> 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.
> Chris.
> -- 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)?
> 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

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