[gmx-users] g_rms using a structure in trajectory as reference

Justin Lemkul jalemkul at vt.edu
Mon May 29 21:13:30 CEST 2017

On 5/29/17 8:55 AM, Francesca Lønstad Bleken wrote:
> Hi,
> I am trying to understand how to best use a chose frame in the trajectory as reference structure for the analysis when using for instance g_rms or g_rmsf.
> For instance, if I want to see how the structure changes with respect to the structure 20 ns after the beginning of the simulation.
> If I understand correctly I can use the .tpr for the md run, but then the input structure is used as reference.
> gmx_mpi rms -s protein-md.tpr -f trajout_noPBC.xtc -o rmsd.xvg
> I have done what I wish to do by dumping the desired snapshot to a .gro with trjconv and using this file for the -s input, and it seems to work fine (but with 2 warning messages that should not be problematic in my case) .
> The warnings are
> WARNING: If there are molecules in the input trajectory file
>           that are broken across periodic boundaries, they
>           cannot be made whole (or treated as whole) without
>           you providing a run input file.
> 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. These guessed numbers might deviate from the mass
>           and radius of the atom type. Please check the output
>           files if necessary.
> Although these warning messages should not be problematic since the trajectory has been fixed so that the enzyme is always at the center of the box and masses and radii are not of interest in just this case, I wonder if there is a better method
> for choosing the reference structure from the trajectory while also keeping the info from the .tpr file. I realize I could make a new tpr with grompp, but in this case I am making a new .tpr and not keeping the info from the last.

The .tpr file is used to determine masses, bonded connectivity, and periodicity 
settings.  A properly re-imaged trajectory shouldn't have anything to do with 
the latter two, but masses are important.  As the warning above states, 
assumptions will be made.  If this is a normal protein, there's probably no 
issue in doing this.  But it's trivial to simply create a new .tpr file from the 
coordinates in your chosen snapshot for the purpose of analysis.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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