[gmx-users] RMSD command line doubt
jalemkul at vt.edu
Mon Apr 29 14:23:48 CEST 2019
On 4/28/19 9:53 PM, Neena Susan Eappen wrote:
> Hello gromacs users,
> My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro).
> Q1) So, I don't understand the purpose of giving .tpr input file (which was the input structure file before production mdrun) as a structure file in the command.
> gmx rms -f peptide.trr -s peptide.tpr -o rmsd.xvg
The .tpr contains the topology (including masses for fitting) and the
reference structure to which the fit is performed.
> Q2) When I use final structure .gro file (after production mdrun), I get the following warning:
> Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files.
This message is printed any time a coordinate file is used as reference.
For a standard protein simulation with nothing fancy about it, the
guessed masses are fine. If you want to be 100% sure you're getting the
right masses, generate a new .tpr file from the desired coordinate file
and use it for analysis.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users