[gmx-users] Result analysis of protein water

Smith, Micholas D. smithmd at ornl.gov
Fri Sep 8 18:38:30 CEST 2017

First: Welcome to the wonderful world of MD. 

Second, 10ns for a 164 residue protein is nowhere near enough simulation time. If you are looking for just small modifications, you could do an alignment of the backbones of the proteins in each trajectory and compare all frames to all-frames using the rmsd (you'd end up with a matrix of rmsd values comparing trajectory 1 to trajectory 2). 

Other things to consider are: salt-bridges, hydrogen-bond networks, and secondary-structure measurements (STRIDE or DSSP).

Good Luck.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Deep kumar <deepak.choubey86 at gmail.com>
Sent: Friday, September 08, 2017 12:30 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se; gmx-users at gromacs.org
Subject: Re: [gmx-users] Result analysis of protein water

Hello All,

I have performed MD on a protein water for 10ns, protein with total 164
residues in two chains. I have got the result graphs of radius of gyration
and rmsd for both wild and mutant. Wanted to attach the graphs but could
not due to bytes limit. There is one residue mutation (M -> T) in the
protein. I am new to MD analysis. Could you please let me know how to know
if the mutation is causing any conformational change. I can look at the
trajectories obtained of wild and mutant type, but to make accurate
analysis I would need more information. Also, please do share with me how
can i do more analysis to see the effect of mutations. Please let me know
if I need to provide more information.

Thanks & Regards.
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