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 > > > > > > > > > > -- > > 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 > > > > > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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? 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