[gmx-users] RMSD calculations by g_rms

Xavier Periole X.Periole at rug.nl
Mon Dec 31 12:07:07 CET 2007

On Mon, 31 Dec 2007 16:22:40 +0530
  Monika Sharma <mon_sharma at research.iiit.ac.in> wrote:
> Dear All, 
> I have two queries regarding the rmsd calculations of gromacs run.
> 1. I was trying to calculate rmsd for 3ns run of my protein system. I
> did it in two ways: VMD (RMSD Traj tool) and g_rms. I found great
> differences in pattern. I know that VMD gives values in angstrom,
> instead g_rms gives values in pm. The thing is that in case of VMD traj
> calculation, I get the rmsd values in decreasing order from around 5.5
> to 0.5 angstroms. But in g_rms I get in ascending order from 0.0 to
> 0.5nm. And this should be the right thing (ascending order). This thing
> really confuses me that why is it happening? Has anyone also encountered
> such problem??
> I am using xtc for VMD.

g_rms and VMD should the exact same result. You might check the reference
frame you use and make sure you fit your protein using the same set of

> 2. I have given two consecutive 3ns runs in continuation. first for 3ns,
> then next again for 3ns. In latter, I used unconstrained-start=yes. When
> I am concatenating these xtc files, to get total of 6ns, and then doing
> g_rms, I am getting a dip at 3000 and there it seems to follow earlier
> pattern of VMD.
> that 1 to 3000ps- values of rmsd decreases from 0.5 to 0.005 nm,
> then 3001 to 6000ps - values of rmsd increases from 0.0698 to 0.248 nm.

Check again your reference frame, and you may have made a mistake in your
continuation run, I mean the way you actually continued it.

> In case of alone rmsd calculations, 3ns rmsd showed increasing
> deviations from 0.0005 to 0.509 nm.
> 6ns run rmsd too showed increasing deviations from 0.00 to 0.248nm 

This does not look like a regular continuation run. But again you
reference frame might be the problem.

> But when I am concatenating them, then the 3ns run showed deviations
> down (different from its original) and 6ns showed up (similar to its
> original).

Then the reference frame is not the problem but the way you continued.
Do you fit your protein before the rmsd calculation?
> I really dont know what is happening and why?? Where the things are
> going hay-ward??
>For g_rms, I am using backbone for least square fit and protein for rmsd
> calculation. Similar pattern in all.
> Any kind of suggestions are welcome..
> Regards,
> Monika
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list