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

From: Duke, Robert E Jr <>
Date: Wed, 7 Dec 2011 03:11:13 +0000

Once again, if memory serves, it doesn't so much ignore the atoms_per_molecule info as it basically chooses to override it, unless you turn the feature off. The distinction, at least in my mind, is that I believe I did check for a well-formed prmtop in regard to these numbers, even when I didn't use them. I don't remember what happens with the solvent_pointers section. I'll try to remember to actually look at the code tomorrow; I expect it is pretty obvious what pmemd is doing in terms of parsing the prmtop. I do sort-of remember that some of the interesting scenarios arose due to unexpected or unanticipated order of things in the pdb being fed into xleap. All this stuff got to be really important to me due to performance implications about how you divide up molecules between processors, as well as extra points framing implications. But I also did have an assortment of users with unusual pdb's, and I think the fix did help them; I no doubt am not remembering everything though...
Regards - Bob

From: Jason Swails []
Sent: Tuesday, December 06, 2011 7:01 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] FW: [AMBER] Issue with running sander with SHAKE

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
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Received on Tue Dec 06 2011 - 19:30:03 PST
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