First off, you should keep this on the emailing list. I have included the emailing list in the reply. No need to take it to private email.
Did you read the link that I sent with the reply? You even have the simulation box visualised with the vmd screen shot you sent, so that should be a big clue to you what is going on. Have a play with the vmd periodic images tab, it should very quickly make sense. From what gmx distance says, I don't think you need to use any pbc processing before doing the calculations, it takes pbc into consideration. The processing you did has probably messed things up, most likely the nojump. And the graphs indicate this fact too. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 24 Oct 2018 at 09:32, Antonio Carlesso <antonio.carle...@gu.se> wrote: > Dear Warren, > > I am a PhD student at the University of Göteborg (Sweden). > > > Since you should be an MD expert I would like to ask you one more stuff > regarding this thread (hope I will not bother you): > > > https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg34909.html > > > > > > > > > > Do you have any reason why calculating the distance over time between > two pair of atoms (Oxigen of the ligand VS nitrogen of the Lysine in the > protein) using gmx distance in GROMACs (Figure 1) and VMD(figure 2) does > not match ? > > > *Figure1.* Values obtained with gmx distance in GROMACS > > > > > *Figure 2.* Value obtained for just one of the previous graph (green one) > using VMD. > > > > > > for my believe the ligand is actually moving away (picture below). > > > > > > Thank you for your possible help! > > > > Best regards, > > Antonio > > > > > > p.s. to deal with PBC I first make my system “whole” , extract the first > frame from the trajectory to use as reference, and then use trjconv -pbc > nojump with that first frame as reference > > aprun -n 1 gmx_mpi trjconv -s md_0_500.tpr -f md_0_500.xtc -o > md_0_500_whole_dt50.xtc -pbc whole -dt 50 > > > > aprun -n 1 gmx_mpi trjconv -f md_0_500_whole_dt50.xtc -s md_0_500.tpr -b > 0 -e 1 -o 1st_frame.gro -pbc mol –center > > > > aprun -n 1 gmx_mpi trjconv -s 1st_frame.gro -f md_0_500_whole_dt50.xtc -o > md_0_500_whole_dt50_nojump.xtc -pbc nojump > > > > -- 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-requ...@gromacs.org.