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