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

Eric Smoll ericsmoll at gmail.com
Fri Jul 13 23:02:05 CEST 2018

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.


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.
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