[gmx-users] g_rms matrix between wt and mutant

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 12 16:29:40 CEST 2011

Shay Teaching wrote:
> Hi all,
> (Gromacs 4.0.7): I am trying to make rms matrix between one Wt 
> trajectory and one mutant trajectory using the following command:
> g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n 
> wt_backbone.ndx
> The file wt_backbone.ndx contains the backbone of the protein (Backbone 
> indices are identical between wt and mutant).
> The result is that I am getting a well deserved error saying that wt.xtc 
> and mutant.xtc has different number of atoms (the tpr itself):
> Fatal error:
> Second trajectory (76128 atoms) does not match the first one (76129 atoms)
> So the question becomes: Is there a (convenient) way to produce 
> rms-matrix between wt and mutant?
> Or perhaps circumvent this problem in some other way?

Use trjconv to write out new trajectories containing only backbone atoms of each 
protein, then use tpbconv to write a .tpr file with only backbone atoms in it 
(using index groups, if necessary).  Then run g_rms again with these new 
trajectories and .tpr file.  Everything should match if the indices are chosen 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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