On Aug 16, 2013, at 11:39 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Fri, Aug 16, 2013, Ross Walker wrote:
>
>> So I am proposing that we have code in rdparm that detects zero VDW radii,
>> prints a warning message about it and then adjusts these radii in the code
>> to 0.0000001.
>
> I don't understand how/why this fixes any problem. First, you would have
> to get to distances comparable to the radius for such a term to have any
> effect. You would have already very much messed things up by that point.
> Second, atoms like OH have a zero epsilon as well as a zero radius, so
> just changing the radius would have no effect.
I think Ross meant changing the A and B coefficients to 1E-6 or so, not the pre-combined values.
I'm with Dave on this though. I've run many microseconds of net simulation and I've never seen a problem with zero vdW terms in HO atom types. I realize there are some cases where this bug hits you, but as I recall it is a strange case with carbohydrates. I'm wary about just making these changes under the assumption it will have only remedial effects. The problem-case hydrogens in the relevant carbohydrates (and lipid?) force fields should be modified if they represent problems in normal simulation.
I can also quite easily write a quick parmed action to implement these changes without having to hard-code this new convention immediately into every md engine we have.
Also, I think that the amber codes should implement the Amber force field exactly as it is defined in the prmtop. Implicitly changing parameters in the MD codes is a bad idea, IMO. (How hard would it have been to validate chamber if CHARMM took that approach?) So if we decide to implement this change, it should be done in LEaP, not rdparm (but again, I think the LJ terms should be derivable straight from the combining rules).
> Note that Istvan's lmodprmtop hack directly changes the LJ A term from
> zero to 1000. This has the advantage of not assuming any particular mixing
> rules, i.e. it still works when NBFIX like changes have been used.
As an aside, should lmodprmtop functionality be incorporated into parmed and/or cpptraj if it does simple things? (I'm not sure what else it does...)
All the best,
Jason
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Received on Fri Aug 16 2013 - 12:30:02 PDT
