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

[Eric Smoll]

Justin,

Your pdb2gmx appears to exclude all intermolecular interactions for a
molecule with no hydrogen atoms.  For instance, for a molecule with "N"
atoms indexed from "1" to "N," the first line of the generated exclusions
directive has a record with the "1 2 3...N" series.

Is this expected?  Shouldn't intramolecular nonbonded interactions be
permitted at and beyond 1-4 interactions?

Best,
Eric

On Fri, Jul 13, 2018 at 3:02 PM, Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Justin,
>
> Very grateful for the rapid reply and warning.  If you suggest that I
> should tread lightly with polarizable H atoms, I will avoid it altogether.
>
> I will alter my troubleshooting plan and focus on using your edited
> pdb2gmx program (adding to the rtp, of course) to build a core-shell MD
> topology for my problem molecules.  It should be easy to compare with the
> topology I have prepared with my own tools.  They should be identical.
>
> Best,
> Eric
>
> On Fri, Jul 13, 2018 at 2:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>
>> --
>> ==================================================
>>
>> 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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