From: Olaf Lenz (
Date: Tue Jul 30 2013 - 03:43:42 CDT

Hash: SHA1


On 07/29/2013 05:02 PM, Markus Dahlgren wrote:
> Visually the wrapped box looks fine, but when i calculate
> protein-water nonbonded energies, using NAMD Energy, the vdw and
> coulomb energies will jump from -5000 for some initial windows to
> +9.99999e+09 for the remaining windows. Especially the VdW energies
> spike, registering +1e+10. This suggests that the waters are
> overlapping the protein ligand complex.

If there is indeed an overlap, that would be very surprising, and should
of course not happen if the unitcell parameters are set correctly.
Another possible reason for this could be that NAMD and the pbctools
handle PBC differently, which could, for example, cause a bond to be
overstretched and results in very large energies. Are bond energies
counted in the VDW-energy in NAMD?

> I dont know how to get around this problem. If anyone is
> experienced with pbc tools and could give me some advice or help,
> it would be greatly appreciated. I could supply dcd files, but they
> are of about 1GB total size.

Is it not possible to reduce the size of a dcd file, e.g. by putting
only a single time step into the file? It is very hard to debug your
problem without the actual case.

- --
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
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