Re: [gmx-users] RMSD, two simulations

On Thu, 26 Jun 2008 13:38:30 +0200 Michal Kolinski <[EMAIL PROTECTED]> wrote: Dear Users, The closest tool to your need is g_rms using the option -m, which generates a matrix of rmsd between all pairs of conformations present in the trajectory. To compare the two trajectories you should concat

Re: [gmx-users] RMSD, two simulations

Hi Michael, g_rms should do the trick. First create an index file having an atom group identical in both systems. Then, g_rms -s ref.pdb -f1 trj1.xtc -f2 trj2.xtc -m rmsd.xpm gives you an rmsd matrix with entry ij given by RMSD[(frame i of trj1),(frame j oftrj2)]. The diagonal of that matrix shoul

[gmx-users] RMSD, two simulations

Dear Users, I've created two different models of the same transmembrane protein. These two models were created using homology approach using two different templates (both with similar sequence similarity to the sequence of the target protein). Next, I did two separate 25ns simulations of th