Hello, I ran a 100-ns long simulation of a small protein (trp-cage) at an elevated temperature. I analysed the distance between periodic images using
g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi The output shows that there are situations when the closest distance between certain atoms is much lesser than 1 nm. Conventional wisdom says that if this happens the simulation results are questionable. Is this completely true? If this is indeed true, how would I ensure that this does not happen again? I have posted the output of g_mindist at http://postimg.org/image/bnc0ej3nb/ Any comments and clarifications are highly appreciated Thanks, -- 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
