- Expected values are estimated. For example İf the structure is reach to converge at last 100 ns ( all simulation time is 200 ns), then in theory, diffusion coefficients will dont change at last 100 ns. -I have only one diffusion coefficient for each 10 ns. I have 20 diffusion coefficients during all simulation time. -I controlled all msd.xvg. They are linear. The plot I sent is diffusion versus time. (Please see it again). It isnt msd vs time - I tried to increase sampling. The results are same approximately. Commands for trestart to 1000 ps: Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 10000 # D[ Protein] = 0.1091 (+/- 0.0212) (1e-5 cm^2/s)=13.line from msd.xvg Command for 2.diffusion:g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 10000 -e 20000 # D[ Protein] = 0.0679(+/- 0.0013) (1e-5 cm^2/s) Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 20000 -e 30000 ... Command for 3.diffusion:g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 190000 -e 200000 2013/3/29 Justin Lemkul <jalem...@vt.edu>
> > > On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote: > >> The simplest advice is to increase sampling. >> >> > I think the OP needs to describe what the system is in greater detail. > For a simple liquid, I would opine that 200 ns is normally vast overkill. > For a membrane, it may not be enough. There's just no way to say. > > -Justin > > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
