[gmx-users] RMSDs between pairs of frames in 2 trajectories

[Abramyan, Tigran]

Dear Sir/Madam,


I would like to check the convergence between two trajectories. For that at each time t I am comparing two frames, frame1-traj1 vs frame1-traj2, etc. As far as I understand the following gromacs command should do what I need:


g_rms -f traj1.xtc -f2 traj2.xtc -s protein.tpr -m rmsd-matrix.xpm -dt 10


Please let me know:


(1)  If this command will do what I want.

(2)  If I need the .tpr file of the second trajectory via -s2  (should be the same .tpr file, correct?).

(3)  What is the fastest way to select only a range of residues/atoms for such comparison?


Thanks,

Best,

Tigran


--
Tigran M. Abramyan, Ph.D.
Postdoctoral Fellow, Computational Biophysics & Molecular Design
Center for Integrative Chemical Biology and Drug Discovery
Eshelman School of Pharmacy
University of North Carolina at Chapel Hill
3219 Marsico Hall, Campus Box 7363
125 Mason Farm Road
Chapel Hill, NC 27599-7363
Email:  tigran at email.unc.edu