Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd?
Commands for trestart to 20 ps: 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 10000 -e 20000 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20000 -e 30000 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190000 -e 200000 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 10000 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 10000 -e 20000 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 20000 -e 30000 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 190000 -e 200000 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban <vvcha...@gmail.com> > > > > > 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 -- Ahmet Yıldırım -- 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
