Re: [gmx-users] RMSD calculations by g_rms

2008-01-01 Thread Tsjerk Wassenaar
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

[gmx-users] RMSD calculations by g_rms

2007-12-31 Thread Monika Sharma
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

Re: [gmx-users] RMSD calculations by g_rms

2007-12-31 Thread Xavier Periole
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