If the error bar exceeds the absolute value of diffusion coefficient, just round the number, as I exemplified below.
The error bar should correspond to the last digit of the result value, e.g. 5 +/ -2; 0.0002 +/- 0.0001; 0.4E6 +/- 0.2E6, etc. My immediate guess is that the problem in the code is somewhere with rounding. On Wed, Jul 22, 2015 at 1:49 AM, Ganesh Shahane <[email protected]> wrote: > 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 <[email protected]> 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 >> <[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]. > > > > > -- > 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].
