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

[MD]

Hi Mark,

I looked the combined trajectory with VMD by loading the gro and xtc files,
and the ensemble looks messy (the ligand is flying away from the protein).
I am not sure which step could be causing the issue. But I want to describe
what I have done to the trajectory file from the beginning and hoping if
you could spot anything I did could be causing the issue?

After harvested the md.gro and md.xtc, I tried to correct the overflowing
issue with the following command:
gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -ur compact

Then I trimmed each trajectory file to ignore the first 10 ns.
gmx trjconv -f md_noPBC.xtc -s md.tpr -n md.ndx -pbc nojump -dt 50 -b 10000
-e 200000 -o md_round1_10-200ns.xtc

Then I combined the trajectory files together with the command I described
earlier (pasted below):
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_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

Best,

MD

On Tue, Jan 22, 2019 at 10:19 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > > > > > --
> > > > > > 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.
> > > >
> > > --
> > > 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.
>