Re: [AMBER-Developers] FW: [AMBER] Issue with running sander with SHAKE

From: Jason Swails <>
Date: Tue, 6 Dec 2011 22:01:56 -0500

On Tue, Dec 6, 2011 at 9:36 PM, Duke, Robert E Jr <>wrote:

> If memory serves, I did hit some problems with incorrect molecule
> definition in the prmtop in pmemd development, and I responded by basically
> creating a default mode in pmemd whereby pmemd checks over the bonding
> patterns and redefines molecules. This definitely created differences in
> the virial, but struck me as much more correct (I believe Darden concurred;
> we discussed it). I did also leave the old mode intact, but you have to
> request the old mode by setting a new namelist variable,
> no_intermolecular_bonds, to 0. There were also implications for frames
> definitions in extra points, so when using extra points ff's, setting
> no_intermolecular_bonds to 0 was not permitted. Anyway - just a head's up
> - I think pmemd by default already handles this issue.

Only partially. It does not handle the case where SUM (ATOMS_PER_MOLECULE)
!= NATOM (which is a badly-formed topology file in the first place). But I
think that means it doesn't completely ignore the ATOMS_PER_MOLECULE and
SOLVENT_POINTERS sections, right?

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Tue Dec 06 2011 - 19:30:02 PST
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