[gmx-users] RMSD calculations by g_rms
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
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..
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XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
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