Hi Justin, thank you so far. Now I got some more specific questions regarding g_msd I got my trajectory from 0-30ns. So far it should to be "correct".
I was analyzing this trajectory with g_msd and the following command: g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 15000 -endfit 16000 -o D_coeff g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 15000 -endfit 17000 -o D_coeff g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 15000 -endfit 18000 -o D_coeff and so on I observed an slight linear decreasing diffusion coefficient. The error bars instead were increasing (starting at -beginfit 15000 -endfit 23000) dramatically. Why do I observe such a behavior? Is this the reason: http://gromacs.5086.n6.nabble.com/MSD-and-self-diffusion-td4411869.html In addition to that I analyzed the trajectory every 1 ns: g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 1000 -endfit 2000 -o D_coeff g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 2000 -endfit 3000 -o D_coeff g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 3000 -endfit 4000 -o D_coeff Here I observed extreme fluctuations starting at 25ns. The errors bars starting at 27ns were huge. Why do I observe these extreme error bars and fluctuation for the last 3/5 ns? I checked my whole trajectory (g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000) as well, but it is a straight line, without any observable curves. Thank you for your comments and help. Daniel -- View this message in context: http://gromacs.5086.n6.nabble.com/g-msd-additional-information-tp5003684p5004845.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
