"g_integrate" should be "g_analyze" below. Sorry.
On Fri, Jul 5, 2013 at 12:20 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > Use this command line: > > -- g_velacc -nonormalize -acflen 2001 > -- g_integrate -f vac.xvg -integrate > -- Multiply the resulting value by 333.333, the result will be > self-diffusion coefficient expressed as result * 10^(-9) m^2/s. > > The velocities should be written down at least every 10fs during MD. The > required trajectory depends on system viscosity. The higher it is, the > longer trajectory (and larger acflen) is necessary for relevant results. > > Dr. Vitaly V. Chaban > > > On Fri, Jul 5, 2013 at 11:10 AM, David van der Spoel <sp...@xray.bmc.uu.se > > wrote: > >> On 2013-07-05 10:50, Ishwor wrote: >> >>> I have taken the fit for 2ns in Einsteins curve to calculate the >>> diffusion >>> coefficient but when i take the values up to 100 ps for velocity auto >>> correlation i get the matching result...Is it good to do such thing? i >>> will >>> be happy if you guide me. >>> I have attached the graph of VAC herewith. >>> Thanks >>> <http://gromacs.5086.x6.**nabble.com/file/n5009582/vac.**jpeg<http://gromacs.5086.x6.nabble.com/file/n5009582/vac.jpeg> >>> > >>> >>> >>> >>> -- >>> View this message in context: http://gromacs.5086.x6.nabble.** >>> com/g-velacc-**tp5009541p5009582.html<http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009582.html> >>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >>> >>> The graph does not show the tradition ripples. If this is for water the >> result could be ok with 100 ps, but you still need to have decent sampling >> (e.g. 20 fs) of the velocities since they change rapidly. >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >> -- >> 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> >> > > -- 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
