[gmx-users] Re: Specific question regarding SPC water model
jalemkul at vt.edu
Tue Jun 4 03:04:22 CEST 2013
On 6/3/13 8:12 PM, Someone Else wrote:
> Thanks for the answer.
>> You're introducing atomic overlap and thus an energetic singularity from
> the infinite Coulombic attraction.
> Is there anything I can do with this?
> I posted this question because I'm trying to run a Monte Carlo simulation
> of a water box but eventually it finds the global energy minimum (-Inf) and
> can't escape from it.
That sounds like something done outside of Gromacs, is it not? I would think
that properly accounting for Coulombic interactions would have prevented this
from occurring, but I don't do MC so I can't go beyond speculation.
> 2013/6/4 Justin Lemkul [via GROMACS] <ml-node+s5086n5008760h67 at n6.nabble.com
>> On 6/3/13 7:49 PM, tnorgd wrote:
>>> Dear group,
>>> I am not sure how SPC energy actually works - is there really just one
>>> interaction - just between two oxygen atoms?
>> Yep. A lot of force fields work like that. Given the size of H atoms
>> to their heavy atom counterparts, the heavy atom to which they are
>> generally governs the vdW interactions.
>>> If so, when I place a hydrogen atom of one water molecule at the
>> location of
>>> the oxygen from another water,
>>> the two oxygens are separated by the distance of H-O bond length i.e.
>>> The only VdW interaction is repulsive but finite (and equal ~4E6) but
>>> electrostatic between H and O is -Inf = 1/0.0
>>> What's wrong?
>> Nothing. That makes perfect sense. You're introducing atomic overlap and
>> an energetic singularity from the infinite Coulombic attraction.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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