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

[Mark Abraham]

Hi,

I can't tell, because I don't know what you did with the xtc files
beforehand. But you should follow my earlier advice and visualize the
combined trajectory and observe that this may be your problem before
talking about it further. :-) Then see
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#suggested-workflow

Mark

On Tue, 22 Jan 2019 at 16:06 MD <refmac5 at gmail.com> wrote:

> 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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