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.abra...@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 <refm...@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.abra...@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 <refm...@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.abra...@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 <refm...@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? 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