[gmx-developers] dihedral restraints and domain decomposition
mark.j.abraham at gmail.com
Tue Dec 10 00:53:38 CET 2013
With what version? There were some fixes in 4.6.4 that might be relevant.
On Tue, Dec 10, 2013 at 6:12 AM, David Mobley <dmobley at gmail.com> wrote:
> Dear Devels,
> We've been running some of our usual absolute binding free energy
> calculations using distance, dihedral, and angle restraints, this time on a
> larger system than normal (100k+ atoms).
> What we've found in this situation is that we get crashes reliably due to
> the dihedral restraints when running with domain decomposition. The errors
> are typically not helpful (LINCS warnings preceding a crash, sporadic
> domain decomposition errors, etc.). However, we've established that these
> problems apparently go away using particle decomposition.
> So, this is to ask: Are there expected issues with dihedral restraints and
> domain decomposition? (We apply restraints between our ligand and reference
> atoms in the protein). If what we're doing is not advised, it would be nice
> to know.
> David Mobley
> dmobley at gmail.com
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