[gmx-users] msd and diffusion coefficient and getting unfolded trajectory

[Ananya Debnath]

Hi,

 I did the calculation for water on both sides of bilayer. It is
unlikely that water molecules
donot cross the boundary. May be I need to wait for longer run such
that molecules go out of box.
I will check that. Thank you very much for your suggestions.

 Regards,
 Ananya.





Ananya Debnath wrote:
>  Hi,
>
>   I want to calculate MSD (mean square displacement) for DPPC-WATER
> bilayer system, without using g_msd tool in gromacs, but using any
> other code, I
> need a trajcetory which is unfolded.
>
>>From mails in mailing list I understand that people use trjconv -pbc
> nojump, to remove pbc.
> So I used pbc = xyz in .mdp file, and then
> trjconv -f traj.trr -s topol.tpr -o trajout.trr -pbc nojump
>
> Then if I calculate MSD (by my own code) from the trajout.trr , the
> result is same if I calculate from the original traj.trr file.
>
> Seeing the result I am confused, because -pbc nojump sholud stop the
> molecule from jumping across the box, then how can the MSD be same if
> it is with pbc?

Maybe your trajectory does not have your relevant RMSD groups crossing
the PBC, so trjconv is not doing anything relevant?

Mark