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

[MD]

Hi Mark, yes that makes sense. Then how can I make trjconv avoid from
writing protein+ligand in different cells?
Ming

On Tue, Jan 22, 2019 at 9:59 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> No, length has nothing to do with whether mdrun or trjconv may have written
> different rounds in different representations (e.g. protein+ligand in the
> same periodic cell, or different cells).
>
> Mark
>
> On Tue, 22 Jan 2019 at 15:40 MD <refmac5 at gmail.com> wrote:
>
> > 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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