[gmx-users] Regarding msd

[rajat desikan]

Hi,
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>
wrote:

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