I have a strong belief that an error bar for such numbers exceed the diffusion coefficient values.
Newer gromacs versions (or is it just because of a double-precision compilation?) output more digits. I do want to hope these digits are meaningful.... If I got this situation, I would report 10^(-8)cm^2/s. On Tue, Jul 21, 2015 at 2:14 AM, Ganesh Shahane <[email protected]> wrote: > Hi! > > I am using gromacs version 4.5.5. The values are different. The value > displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value > displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s. > > As you can see, both values are quite close though the value in chol.xvg > doesn't appear to be round up. > > On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury <[email protected]> > wrote: >> >> Hi!! >> >> Are the values different? Can you show us both the values? >> I presume both values would be same. >> The value in the xvg file would be round up. >> >> Chandan >> >> >> On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban <[email protected]> wrote: >> >> > which version fo you use? >> > >> > >> > >> > >> > >> > On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane >> > <[email protected]> wrote: >> > > Dear Gromacs Users, >> > > >> > > I have performed a simulation of a POPC+Cholesterol bilayer. I wish to >> > know >> > > the diffusion constant of a particular cholesterol molecule. Towards >> > this, >> > > I performed a g_msd using the command as follows- >> > > >> > > g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n index.ndx >> > -mol >> > > chol.xvg >> > > >> > > where index.ndx contains a single index for the cholesterol atoms in >> > > question. In the end, I got 2 different values of diffusion constant, >> > with >> > > one of them being displayed on the terminal screen and the other value >> > > in >> > > the chol.xvg file. >> > > >> > > Does anyone have any idea as to which value should be taken as the >> > > value >> > of >> > > diffusion constant? Any help would be appreciated. Thank you! >> > > >> > > -- >> > > Best Regards, >> > > Ganesh Shahane >> > > -- >> > > Gromacs Users mailing list >> > > >> > > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >> > > * For (un)subscribe requests visit >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to [email protected]. >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to [email protected]. >> > >> >> >> >> -- >> >> Chandan Kumar Choudhury >> National Chemical Laboratory, Pune >> India >> >> *"All work and no play makes Jack a dull boy...”* >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >> a mail to [email protected]. > > > > > -- > Best Regards, > Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
