[gmx-users] Grompp error for graphene modeling

‪Mohammad Roostaie‬ ‪ mohammad.r0325 at yahoo.com
Sun May 28 08:01:06 CEST 2017

Thanks Justin for your help. I will modify the force field again to model the particles better.

      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Saturday, 27 May 2017, 23:20:26
 Subject: Re: [gmx-users] Grompp error for graphene modeling

On 5/27/17 3:33 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All,
> I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to add ions to the system, I got this warning:
> WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
>    old:                                          0.151 292880 0.151 292880  new: C    C      1    0.14000  392459.2
> Actually, in the ffbonded.itp file, I put two parameters for C-C which the new one referes to the graphene, and, I cannot change the names in the itp file since the graphene atom names are C.Is this an important warning (May it affect the stability of the system and results)? Or may I use -maxwarn?

Atom *names* and *types* are different beasts.  Types are used in 
ffnonbonded.itp and applied to the atoms found in the topology.  Atom names are 
irrelevant for parameter assignment.  But here you have introduced clearly 
conflicting parameters that will alter the behavior of the conflicting types, 
e.g. any aromatic rings in your peptide will behave incorrectly if you proceed 
with what you're doing.

In general, do not use -maxwarn unless you can clearly articulate why you're 
overriding a serious warning from grompp, not simply to make a problem go away.



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

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