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

[Eric Smoll]

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?

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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> Gromacs Users mailing list
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