[gmx-users] Large Molecule Stability

Justin Lemkul jalemkul at vt.edu
Sun Sep 11 19:50:07 CEST 2016

On 9/11/16 1:43 PM, Evan Lowry wrote:
> 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?

The table limit does not apply to a molecule's size.  The errors that you're 
seeing (please always copy-paste in full rather than editing pieces out - 
there's information there that you're keeping from us) are related specifically 
to 1-4 interactions.  If 1-4 pairs are extending beyond the table limit, that 
means the system is blowing up.  If the simulation is not stable even with dt = 
0.1 fs, then your topology is unsound.


> 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


More information about the gromacs.org_gmx-users mailing list