Hi everybody,
I use these lines in order to get mean square displacement per water molecule.
compute msd water msd/molecule fix msd water ave/time 1 1 4000 c_msd file meansquaredisplacement.dat mode vector
Also I set the fix in this way in order to get the instantaneous (per snapshot) msd. I would like to ask if this msd is the displacement per molecule from the initial configuration or from the previous snapshot or timestep. I ask because I can see that if I plot msd versus time it always increases.
Manual says:
"The displacement of the center-of-mass of the molecule is from its original center-of-mass position at the time the compute command was issued."
Thanks a lot in advance,
Otto