[gmx-users] seeking help for generating combined trajectory files and clusters

[MD]

Thanks Mark.
When you said "mutually compatible periodic representation", did you mean
they all have to have the same length of simulation? E.g. if one of them
has a different length (91ns) and the rest all have 90 ns, the combining
process will go wrong?


On Tue, Jan 22, 2019 at 4:13 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You're comparing to the configurations in -f2, but that will only make
> sense if the contents of the files for each round have mutually compatible
> periodic representation. I suggest you visualise the combined trajectory
> and observe the problem.
>
> Mark
>
> On Mon, 21 Jan 2019 at 17:30 MD <refmac5 at gmail.com> wrote:
>
> > Hi Gromacs folks,
> >
> > I am trying to simulate protein and ligand compound.
> >
> > I did several 200 ns simulations and combined them into one trajectory
> file
> > with the commands:
> > gmx trjcat -f md_round1_10-200ns.xtc
> >  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
> > -settime
> > I set the starting times to be: 10 ns, 190 ns, 380 ns
> >
> > Then I made a RMSD matrix with the command:
> > gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n md.ndx -m
> > md_RMSD-matrix.xpm
> >
> > Then I tried to build clusters with the command:
> > gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm
> md_RMSD-matrix.xpm
> > -method gromos -cl out.pdb -cutoff 0.2 -g out.log
> >
> > There were 120 clusters came back. Except for the first and largest
> > cluster, all the rest of the clusters have a crazily far away ligand
> > compared to where the protein is.
> >
> > I went back to look at each individual xtc from each round and produced
> > their own clusters and they all look good (no huge separation of protein
> > and ligand).
> >
> > If all the xtc files are good on their own, how come the combined xtc is
> > giving me this result?
> >
> > Best,
> >
> > MD
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