> > if I do as you said, I will get only one diffusion coefficient. I want to > calculate one diffusion coefficient for each 10 > ns of the simulation time of 200 ns. That is, I want to get 20 diffusion > values. > > 2013/3/28 David van der Spoel <sp...@xray.bmc.uu.se> > >> On 2013-03-28 10:40, Ahmet yıldırım wrote: >> >>> Dear users, >>> >>> This time, I calculated the diffusion coefficients of protein for each 10 >>> ns of the simulation providing a total simulation time of 200 ns. >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 >>> -endfit -1 -b 0 -e 10000 >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 >>> -endfit -1 -b 10001 -e 20000 >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 >>> -endfit -1 -b 20001 -e 30000 >>> .... >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 >>> -endfit -1 -b 190001 -e 200000 >>> >> >> Set trestart to 10001 (no restarts), or do one run with >> >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 10000 >>
I believe the advice was to increase "trestart" and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- 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
