The simplest advice is to increase sampling.
> Please see plot: > http://imageshack.us/photo/my-images/35/diffusion.png/ > > 2013/3/28 Justin Lemkul <jalem...@vt.edu> > > > On Thu, Mar 28, 2013 at 9:59 AM, 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? > > > > > > > > I see no evidence for a bug, and you should avoid such speculation unless > > you know exactly how the program should behave. Only then, after an > > analysis of known quantities or behavior, can we discuss bugginess. Do > you > > know how g_msd works? Do you know what all of the flags are doing, or are > > you just making adjustments hoping for clarity? You may find the > following > > post very illuminating: > > > > http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html > > > > -Justin > > > > > > > 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