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

[Justin Lemkul]

On 7/13/18 8:14 PM, Eric Smoll wrote:
> 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?

I don't want to guess based on files I haven't seen. There's not much I 
can tell you.

-Justin

> 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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>>

-- 
==================================================

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

==================================================