[gmx-users] .top file molecules directive
jalemkul at vt.edu
Thu Jul 10 18:55:08 CEST 2014
On 7/10/14, 11:03 AM, Aranha, Michelle wrote:
> 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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