[gmx-users] .top file molecules directive

Justin Lemkul jalemkul at vt.edu
Thu Jul 10 18:55:08 CEST 2014

On 7/10/14, 11:03 AM, Aranha, Michelle wrote:
> Hello,
> My system  consists of a carbon nanotube separating two reservoirs of water bounded by 2 graphene sheets at the interface between water and the CNT.
> I build the topology after constructing this geometry using g_x2top . This gives me a file which includes all the interactions for the CNT, graphene and water but in the final directive  I have just 1 molecule, instead of 3 different molecules.
> My question is can this result in artifacts in the system because of the way I'm building the top file? I checked for the bonded and non- bonded parameters in the top file and they seem correct.

What you define as a [moleculetype] in Gromacs has no relevance to the chemical 
definition of a "molecule."  In principle, one could describe any system as a 
single [moleculetype], which may be convenient in some cases.  What truly 
dictates the physics and the validity of the model is the interactions defined 
in the topology.  If those are sound, the bookkeeping is irrelevant.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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