Originally Posted By: rmv
COOR ANAL can handle PBC with orthogonal lattice types, but only computes MSD for single atoms, not the molecular COM.

I see.

Originally Posted By: rmv

By "small", I meant less than ten or so lipids; your system seems okay.

Note that since there is both a short time and long time diffusion, one must care in the fitting to discard either the short time or long time data. Plots of r^2 vs t, esp. averaged over molecules, should make it clear where the slope change occurs.

I am interested in the long time diffusion so I'll drop the short time data. Mhhh, well thinking twice about it, I am probably interested in both parts so I have to calculate it twice wink Also i will cut my simulation into some larger parts and calculate the diffusion only for these parts to compare them against each other.

Thanks for the notes.

Kind regards

Last edited by blubbi; 10/14/10 08:11 AM.