[gmx-users] RMSD command line doubt

Justin Lemkul 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.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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