Hi Monika, Xavier,
You can't really judge a run from the rmsd ;)
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
atoms.
I concur, and Xavier, you hit the spot with referring to the reference
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
On Mon, 31 Dec 2007 16:22:40 +0530
Monika Sharma [EMAIL PROTECTED] 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
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