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

Justin Lemkul jalemkul at vt.edu
Sat Jul 14 04:13:07 CEST 2018

On 7/13/18 9:42 PM, Eric Smoll wrote:
> Hi Justin,
> Using your code to generate the topology for my system still results in the
> distortion of bonds to hydrogen when constraints=h-bonds and emtol=100
> (note that the energy minimization mdp files provided with your paper use
> an emtol of 1000).  However, when I set constraints=none and emtol=100, no
> distortion of bonds to hydrogen occur.  Maybe there is some problem using
> shells with constraints.
> I am going to remove all constraints from my system and check if my system
> is stable with SCF and Lagrangian core-shell molecular dynamics.

You're going to have to use a very short time step, but the constraint 
code is entirely separate from anything dealing with polarization, so I 
have no clue why the two would be connected. Again, happy to 
troubleshoot a real system but it's really hard for me to guess at 
what's going on.


> Best,
> Eric
> On Fri, Jul 13, 2018 at 6:14 PM, Eric Smoll <ericsmoll at gmail.com> 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?
>> 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


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