[gmx-users] treating trajectory for diffusion calculations

[Dave M]

Ah! am sorry, I figured out. Please ignore my mail.
I was using wrong group selection for rmcomm in the command line.

Sorry to all!
Dave

On Thu, Apr 9, 2020 at 11:26 PM Dave M <dave.gromax at gmail.com> wrote:

> Hi All,
>
> I have a coarse-grained simulation box with water and oil phases. Just
> playing with the diffusion 'only on a single particle' (single martini
> coarse bead) gave me different results when I use -rmcomm on trajectories
> with and without -pbc nojump.
>
> NOTE: selected only single bead
>
> Same diffusion results:
> gmx msd  -s md.tpr -n index.ndx -f md.xtc  # D=2.8914 x1e-5 cm^2/s
> gmx msd  -s md.tpr -n index.ndx -f nojump.xtc # D=2.8914 x1e-5 cm^2/s
>
> Different diffusion results:
> gmx msd  -s md.tpr -n index.ndx -f md.xtc -rmcomm #D= 2.491e-15 x 1e-5
> cm^2/s
> gmx msd  -s md.tpr -n index.ndx -f nojump.xtc -rmcomm #D = 7.03e-16 x1e-5
> cm^2/s
>
> Also, I note that -rmcomm D values are very different (factor slow by
> e-15) from when I don't use rmcomm. What is the correct way to treat
> trajectory here before calculating msd? I have run my simulation as
> comm-grps whole system (default option). I am not sure when should I use
> -rmcomm option (in gmx msd) though the MSD numbers look more relevant if I
> don't use this.
>
> Thanks
> Dave
>