[gmx-users] Query of RMSD results

Smith, Micholas D. smithmd at ornl.gov
Wed Oct 29 14:08:29 CET 2014

Which routine did you use for your RMSD calculation: g_rms or g_rmsdist?

If your reference structure was the first frame of your trajectory (the default, I believe), than what your rmsd measure is telling you is that the protein-ligand complex "average" deviation from it's initial conformation is less than the protein on its own (slightly). See chapter 8 of the manual for details on how the calculation is performed. Also look at Maiorov & Crippen, Proteins
22, 273 (1995)

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 Sainitin Donakonda <saigro16 at gmail.com>
Sent: Wednesday, October 29, 2014 8:54 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Query of RMSD results


I performed 20ns MD simulation on 2 types systems

1) Protein only
2) Protein-ligand 1 complex

Then did RMSD analysis on both systems i observed that following RMSD mean
as follows

Protein only : 0.45 nm
Protein-ligand 1 complex: 0.40

Now i am confused how to interpret this result as protein-ligand complex
RMSD is lower than apo form of protein.

Can any body please explain how to explain these results

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