[gmx-users] Regarding msd

[pratibha kapoor]

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.