Yes, for some calculations the error bar values did exceed the diffusion coefficient values.
I am using the double-precision version of gromacs. But then again the question is whether to consider the value displayed on the terminal screen or the one displayed in the .xvg file. On Tue, Jul 21, 2015 at 10:25 PM, V.V.Chaban <vvcha...@gmail.com> wrote: > 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 > <ganesh7shah...@gmail.com> 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 <iitd...@gmail.com> > > 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 <vvcha...@gmail.com> wrote: > >> > >> > which version fo you use? > >> > > >> > > >> > > >> > > >> > > >> > On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane > >> > <ganesh7shah...@gmail.com> 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 gmx-users-requ...@gromacs.org. > >> > -- > >> > 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 gmx-users-requ...@gromacs.org. > >> > > >> > >> > >> > >> -- > >> > >> 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 gmx-users-requ...@gromacs.org. > > > > > > > > > > -- > > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
