[gmx-users] extracting data for individual particles

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 23 03:35:31 CET 2010

Paymon Pirzadeh wrote:
> Hello,
> I have a run with the xtc, trr and edr files available. I would like to
> color a snapshot of my system with respect to rmsd or potential energy
> of my particles. How can I extract the potential energy, rmsd or any
> other needed data from the files available? Is there a specific GROMACS
> command that I can use?

Probably a combination of different analysis tools and probably your own 
scripting would be required.  RMSD per atom can be be plotted with g_rmsf -od, 
but the output is an .xvg file, so you will have to find some way to transfer 
these data into a coordinate file (B-factor field in a .pdb file, for example). 
  Potential energy per particle is a relatively meaningless quantity, since the 
PE is not entirely described by a single particle; it is dependent upon the 
surrounding system, as well.  This sort of thing has been discussed a number of 
times (for example, users wanting the potential energy of just the protein, 
excluding solvent, etc).


> Regards,
> Payman


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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