[gmx-developers] dihedral restraints and domain decomposition

[Mark Abraham]

Hi,

With what version? There were some fixes in 4.6.4 that might be relevant.

Mark


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.
>
> Thanks!
> David
>
>
> --
> David Mobley
> dmobley at gmail.com
> 949-385-2436
>
>
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