[gmx-users] Finding centroid for a bunch of residues

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 6 13:25:13 CEST 2008

vivek sharma wrote:
> Hi there,
> This is the question out of gromacs..but I need it urgently.. and I hope 
> this is the only place where I can get such expert to solve my query...
> while trying to restrict my MDRUN for a particular site of the protein 
> molecule I want to visualize the site and find out the centroid for the 
> particular site......
> Is there any visualization tool that can do the same ..
> I mean Is there any molecular visualization tool that can help in 
> finding out the ...centroid between a group of resuidues ?

You will likely have to write a script that will do this for you.  It can be 
accomplished, for example, with VMD, although my own personal experience with 
such scripting is somewhat limited.  See for example:


That may give you some ideas.


> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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