perhaps, you could make a plot?? it is difficult to understand what you are speaking about.
Dr. Vitaly Chaban On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım <ahmedo...@gmail.com> wrote: > 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
