[gmx-users] Large Molecule Stability

[Evan Lowry]

The molecule is an atomistic kerogen (aromatic sheets with interbonded
oxygen, nitrogen and sulfur). I parameterized the molecule from OPLS and
created the topology with pdb2gmx by modifying the .rtp file. I have
rigorously minimized and checked all the bonds for accuracy. Can a
molecules size effect the nonbonded interactions within the molecule? i.e.
if the molecule is larger than the table limit of ~2.5nm?

Thanks for your help,

Evan L.

On Sep 11, 2016 11:24 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:



On 9/11/16 1:19 PM, Evan Lowry wrote:

> Dear Gromacs Users,
>
> I am working with a very large molecule that has 580 atoms and am trying to
> conduct NVT simulations. Unfortunately, GROMACS is highly unstable with
> this molecule and keeps crashing even with LINCS and a time step of 0.1 fs.
> I have checked and rechecked the structure but keep getting the following
> warning:
>
> WARNING: nonbonded interaction between particles... is larger than the
> table limit...
>
> Is this due to the size of the molecule (+3nm long) or charge groups? I am
> out of simulation options to change and was hoping someone may have some
> suggestions for increasing the stability of the simulation.
>
>
What is this molecule and how did you generate its topology?  Size is not
an issue (580 atoms is not large at all) and we can't comment about charge
groups without knowing more about what you're doing.  Charge groups are
sort of an antiquated notion, anyway.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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