Originally Posted By: rmv
If the lipids were subject to image centering during the simulation, then you must account for that. Otherwise, the r^2 vs. t data will be contaminated by large jumps across the unit cell.

I guess this is best done vie unwrapping the trajectory. Or is there any build in code which is able to detect those jumps. The only way, except unwrapping, I can imagine right now is to check frame for frame if a large translation occurs. But this would be rather time consuming.

Originally Posted By: rmv
In order to have the box size taken from the stored trajectory frames, you must both set up CRYSTAL and use XBOX etc.; the lattice must be orthogonal (all angles 90 deg) which means only CUBIC, TETRAGONAL, or ORTHORHOMBIC lattice types. (The same restriction applies to MERGE COOR UNFOLD; only orthogonal lattice types are supported.)

That's fine for me, my lattice is orthogonal.

Originally Posted By: rmv
Calculating diffusion accurately for just one molecule is highly problematic, regardless of the approach; standard procedure is to average over molecules and/or replicate simulations. Lipids pose bigger challenges due to the presence of short time diffusion based on "rattling in a cage", and long time diffusion based a jump model with lipids changing places. Several replicate simulations might be needed to get statistically meaningful results for a small number of lipids.

Mhh, well my system consists of 86 POPC, 43 POPS, and 43 Cholesterols per leaflet so I guess this counts as small number.


Originally Posted By: rmv
While I haven't had time to clean up them up for the Script Archive, I do have CHARMM inputs, csh batch scripts, and a Fortran90 program which do these steps:

(1) image unfold the coordinate trajectory to a scratch volume (MERGE)
(2) for each molecule, compute the r^2 vs. t difference correlation function (CORREL), in both 3D and 2D
(3) compute D from input r^2 vs t data, in 3D or 2D, with optional finite size correction (cubic only); provides standard errors based on grouping (F90 prog)

Available via email request.


I guess using and modifying your code yields faster a result then writing my own and since you are willing to share it I don't have to re-invent the wheel. Thanks a lot! Mail has been dispatched.

Thanks a lot!
Kind regards
Bjoern