Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi.
Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubi...@gmail.com> wrote: > Hi, > > > > I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see > if the complex is seeing its next periodic image, so I used the g_mindist > command with the -pi option. My command line was: > > g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi > > The output (see below) was stable until ~344ps when there is a jump in the > max internal distance (third column) from ~6nm to ~22nm. After the jump the > numbers are reduced back to ~6nm and remained stable until the run is > completed at 1ns. > > Does anyone know how to explain this jump? Is this a real problem or just a > visualization artifact? Is there a way to avoid such jumps? > > > > Here is the mdp file I used: > > ------run.mdp------ > > integrator = md > > nsteps = 1000000 > > dt = 0.001 > > coulombtype = pme > > vdw-type = cut-off > > tcoupl = Berendsen > > tc-grps = protein non-protein > > tau-t = 0.1 0.1 > > ref-t = 310 310 > > nstxout = 100 > > nstvout = 0 > > nstxtcout = 100 > > nstenergy = 100 > > comm_mode = Linear ; Angular > > comm_grps = Protein > > xtc_grps = Protein > > energygrps = Protein > > ------------------ > > > > Thanks, > > Ifat > > > > The output: > > 343.7 10.813 5.924 16.445 16.445 16.445 > > 343.8 10.809 5.949 16.445 16.445 16.445 > > 343.9 10.804 5.959 16.445 16.445 16.445 > > 344 10.808 5.974 16.445 16.445 16.445 > > 344.1 0.18 21.982 16.445 16.445 16.445 > > 344.2 10.778 5.977 16.445 16.445 16.445 > > 344.3 10.768 5.996 16.445 16.445 16.445 > > 344.4 10.764 6.016 16.445 16.445 16.445 > > 344.5 10.722 6.029 16.445 16.445 16.445 > > 344.6 10.774 6.01 16.445 16.445 16.445 > > 344.7 0.174 21.984 16.445 16.445 16.445 > > 344.8 0.176 21.98 16.445 16.445 16.445 > > 344.9 0.17 22.002 16.445 16.445 16.445 > > 345 0.173 21.981 16.445 16.445 16.445 > > 345.1 0.191 21.954 16.445 16.445 16.445 > > 345.2 0.183 21.958 16.445 16.445 16.445 > > 345.3 0.181 22.012 16.445 16.445 16.445 > > 345.4 0.17 22.054 16.445 16.445 16.445 > > 345.5 0.168 22.054 16.445 16.445 16.445 > > 345.6 0.189 22.039 16.445 16.445 16.445 > > 345.7 0.171 22.007 16.445 16.445 16.445 > > 345.8 0.186 22.031 16.445 16.445 16.445 > > 345.9 0.171 22.077 16.445 16.445 16.445 > > 346 0.187 21.99 16.445 16.445 16.445 > > 346.1 0.173 21.984 16.445 16.445 16.445 > > 346.2 0.181 22.02 16.445 16.445 16.445 > > 346.3 10.82 5.984 16.445 16.445 16.445 > > 346.4 10.81 6.002 16.445 16.445 16.445 > > 346.5 10.819 6.008 16.445 16.445 16.445 > > 346.6 10.813 5.996 16.445 16.445 16.445 > > 346.7 10.781 6.006 16.445 16.445 16.445 > > 346.8 10.793 6.026 16.445 16.445 16.445 > > 346.9 10.745 5.985 16.445 16.445 16.445 > > 347 10.762 5.999 16.445 16.445 16.445 > > 347.1 10.781 5.984 16.445 16.445 16.445 > > 347.2 10.784 6.002 16.445 16.445 16.445 > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
