[gmx-users] Shell (Drude) model for polarization in GROMACS

[Justin Lemkul]

On 7/13/18 4:48 PM, Eric Smoll wrote:
> Hello Justin,
>
> Thank you for the guidance.
>
> Although more testing is needed, molecules where shells are attached to
> every atom appear to be working properly.
>
> The issue appears to be with models where shells are only attached to heavy
> atoms and bonds between hydrogen atoms and heavy atoms are constrained.
> Initial energy minimization tests (emtol = 100) show that bonds between
> heavy atoms and hydrogen in organic molecules slowly stretch or compress
> far more than they should while the network of non-hydrogen atoms maintains
> a sensible geometry.  All atom-drude displacements on the heavy atoms
> converge quickly and are stable.
>
> I am still hunting for whatever topology problem is causing this.  All
> exclusions out to 1-4 interactions between atoms and drudes should be
> properly included (combined action of the moleculetype directive and
> additional exclusions directives).  Thole screening only applies to
> atom-shell pairs so no screening is needed for 1-2 and 1-3 pairs with H
> atoms (no attached shells).  It may be difficult to provide any useful
> guidance without details but troubleshooting suggestions are welcome if you
> have any.
>
> Are there issues associated with adding shells to specific atoms in a
> molecule?  Are simulations that place shells on all atoms (hydrogen and
> heavy) more stable for some reason?  I am going to build a new model where
> shells are attached to all atoms to see if bonds to hydrogen atoms still
> slowly compress/stretch during a tight-emtol energy minimization.

I have never tested a system like that. Our Drude convention does 
exactly what you seem to find a problem - Drudes on heavy atoms and not 
H, with bonds to H constrained. I've never had the issue you're 
experiencing. Without a full test case of complete inputs, I can't tell 
you anything.

Be forewarned - I know of no efforts by me or anyone else to deal with 
polarizable H atoms in GROMACS, and that may conflict with constraints, 
so tread lightly...

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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