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).
-Justin
Regards,
Payman
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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