[lammps-users] Evolution of the center of mass of polymers

Hi,

I have 1000 polymers made up of 200 lennard jones atoms with fene bond
connections. I want to calculate the diffusion coefficient of the
polymers. I can use compute com or compute msd. Compute msd does not
give good statistics as it does not use the values of previous
timesteps so the best way that I see to go about this is to dump the
center of mass coordinates of each polymer and calculate the mean
squared displacement using the com's. However, I am limited to 32
groups which I can use in "compute com". I could dump the coordinates
of each atom and post process to get the polymer center of mass
coordinates but this would mean I will be dumping 200 numbers more in
comparison to just dumping the center of mass of the polymer.

Maybe there are new features in LAMMPS that I don't know to get around
my problem of how to efficiently obtain the center of mass of more
than 32 polymers. Any help or suggestions is very much welcomed.

Jan-Michael

Check out compute com/molecule and compute msd/molecule.
If you want to do continuous time averaging from a bunch
of t=0 starting points, then I think you do indeed need to post
process that, e.g. from compute com/molecule data.

Steve