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

From: Yong Duan <>
Date: Tue, 06 Dec 2011 19:48:48 -0800

I actually think molecule-based pressure scaling may fail in some cases.

Suppose the system is a large unfolded protein. For simplicity, the COM of
the protein is at the origin. So, it won't move in pressure scaling.
Because scaling of the COM of the water molecules necessarily moves the
water, but not the protein, you can potentially have the scenario of a few
unlucky water molecules bump into the protein. For large protein, this may
cause failure if there were already water molecules in close contact with
the protein before the scaling.

With the increase of system size and complexity (oligomers, for example),
we may see this sort of things more often.

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/6/11 6:36 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.
>Regards - Bob
>From: case []
>Sent: Tuesday, December 06, 2011 5:43 PM
>To: Breuer, Marian
>Subject: Re: [AMBER-Developers] FW: [AMBER] Issue with running sander
>with      SHAKE
>On Tue, Dec 06, 2011, Breuer, Marian wrote:
>> Of course, this does
>> unfortunately not provide any explanation why sander seemingly bothers
>> about molecules (rather than residues) in the first place.
>Sander handles constant pressure simulations via a "molecular virial"
>in which internal forces inside a "molecule" can be ignored.  For constant
>pressure runs, it also distributes the atoms among processors, dividing
>along molecule boundaries.  But this code (and similar code in LEaP)
>that the atoms in a molecule are contiguous in the atom list.
>> Andrew Voronkov (who described a similar problem on the mailing list
>> recently) told me that in his system (protein + ligand + zinc atom) the
>> zinc atom was covalently bound to the protein but the cofactor was not,
>> and as he described on the mailing list, the solution to his problem
>> was to place the zinc atom between protein and cofactor rather than
>> after the cofactor. I'd then assume that this was an analogous situation
>> (avoiding bound atoms to be split in the atom list).
>I agree that this is the same problem.
>I'm cc-ing this to the Amber developers' list; it is rather odd that this
>problem has not shown up earlier, since the code involved is quite old.
>On the to-do list (increasing level of difficulty):
>1. LEaP definitely should check for this, and certainly should not create
>an ATOMS_PER_MOLECULE data structure that is incorrect.  At an even more
>basic minimum, Dave Cerutti's [or Jason's] prmtop validation/editing
>could also flag this problem.]
>2.  The Users' manual should document this requirement, and error messages
>about its violation should point to such documentation.
>3.  The pmemd sanity check on ATOMS_PER_MOLECULE should be backported to
>4. (Longer term) better barostats use an "atomic" model for volume
>fluctuations, avoiding the rather arbitrary division into molecules.
>> But an additional reason for my slow reply: my memory of the code is
>> the splitting of atoms should depend on residues, not molecules.  So I
>> to see if I can understand how your original problem (with > 14 nodes)
>As per usual, my memory was wrong.  For constant pressure runs, splitting
>of atoms among processors depends on molecules, not residues [as comments
>in the set.f file (that I think I wrote!) clearly indicate.]  If the
>information in the prmtop file is wrong, things can be badly messed up.
>...thanks for your input....dac
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Received on Tue Dec 06 2011 - 20:00:03 PST
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