I am trying to caculate MSD-center of mass of sukpnated polystyrene.
I have used below to calculate MSD in previous versions successfully for 500 frames .
gmx msd -f pss10_500_1000.xtc -s pss10.gro -n pss10.ndx -o msd-pss10.xvg
But now I get below when I try to run this and it does not giving any out put.Please advice.
“Notofocation I get”: Available static index groups:
** Group 0 “Group” (274891 atoms)** Specify any number of selections for option ‘sel’ (Selections to compute MSDs for from the reference): (one per line, for status/groups, ‘help’ for help, Ctrl-D to end)
Is there any advice that you can give me to try?
I have total 274891 atoms in the index file ,In earlier reply I just included only the intial lines.I have removed around 1000 sodium counter ions and created the index file having only 274891 atoms in polymer chains.In gro file it has the total atoms with sodium 275891.
First, I would recommend making a selection group for the atoms you are interested in calculating the MSD of, i.e. the polystyrene - not the solvent.
It’s a bit unclear to me, where the program stops. You just say it’s “not giving any out put”, but you don’t explicitly say that you have provided the numbers of the selection groups you want to analyze. Have you? If you did so, I think the problem is that it might be slow (and quite irrelevant) calculating the MSD of all 274891 atoms. How long did you wait?