[gmx-users] RMSD calculations by g_rms

Monika Sharma mon_sharma at research.iiit.ac.in
Mon Dec 31 11:52:40 CET 2007

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.

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.

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 

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

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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