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

Abhishek Acharya abhi117acharya at gmail.com
Mon May 29 16:12:32 CEST 2017


AFAIK, only coordintes of the reference file is uses for rmsd and rmsf
calculations. So you can do what you have already mentioned.
However, the choice of input structure may be different for rmsd and rmsf
calculations. Both can take any input coordinate (with same number of
atoms), but for rmsd, the general use case would take the starting frame
and calculate the rmsd for full trajectory to see the overall convergence
to equilibrium structure compared to the input structure.

For rmsf, it would make more sense to take a frame from the equilibrated
segment of the trajectory and run the rmsf analysis on the equilibrated
segment alone.

Abhishek Acharya

On May 29, 2017 18:26, "Francesca Lønstad Bleken" <
francesca.l.bleken at sintef.no> 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.
> I hope I have managed to explain my question.
> Best,
> Francesca
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