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

[Mark Abraham]

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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