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

[Justin Lemkul]

On 7/15/18 9:14 PM, Eric Smoll wrote:
> Justin,
>
> No problem.  That makes sense.
>
> Can I send my atp, rtp, itp, and gro files used with the pdb2gmx from your
> drude branch off-list?

Yes, please send a full, self-contained example with any relevant 
commands or information to reproduce whatever problem you're having.

-Justin

> Best,
> Eric
>
> On Fri, Jul 13, 2018 at 8:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>
>> ==================================================
>>
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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

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