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

Francesca Lønstad Bleken francesca.l.bleken at sintef.no
Mon May 29 14:55:50 CEST 2017


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.

I hope I have managed to explain my question.



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