[gmx-users] Regarding msd

rajat desikan rajatdesikan at gmail.com
Wed Oct 8 09:22:00 CEST 2014

You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong
for calculating the msd.

On Tuesday, October 7, 2014, pratibha kapoor <kapoorpratibha7 at gmail.com>

> Hi all
> I have created my own code for msd calculation and would like to verify it
> from g_msd. I have created pdb files using trjconv -center -pbc whole
> option. Can I use the coordinates in pdb as such (with no
> wrapping/unwrapping/shifting) for running my code? or does the inbuild
> g_msd program modifies them (shift)?
> My msd values are not matching with the g_msd values. I suspect that
> discrepency in the pdb file creation since the values obtained from my
> program agrees with manual calculation (of some dummy values).
> Any suggestions are highly welcomed.
> --
> 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-request at gromacs.org <javascript:;>.

Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

More information about the gromacs.org_gmx-users mailing list