[gmx-users] How to analyse the results of MD

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 3 13:58:30 CEST 2010

rekkha nivethitha wrote:
> Hi..
> I have performed molecular dynamics simulation of protein-protein complex.
> How to interpret the results of potential energy, kinetic energy, total 
> energy, temperature,
> RMSD, rmsf, radius of gyration.
> I got the graphs for the above said parameters in xmgrace..
> I need to interpret the graph.
> Can u help me..
> Looking for your valuable reply.

The better approach to simulation is to understand what type of information you 
will need to answer whatever question it is that you're answering.  If you 
simply don't know what those terms are, any textbook on MD (or probably even 
basic physics) will explain them.  But again I must emphasize that it is of no 
use to you to blindly run analysis and then hope for something useful later.


> Thank u.
> -- 
> S.T.B. Rekkha Nivethitha
> MPhil, Department of Bioinformatics,
> Structural Biology Lab,
> Bharathiar University,
> Coimbatore - 46.


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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