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

[Mark Abraham]

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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>