[gmx-users] Topology file and itp file

Justin Lemkul jalemkul at vt.edu
Fri Apr 21 14:22:00 CEST 2017

On 4/20/17 4:37 PM, lan hoa Trinh wrote:
> Dear Mark,
> I equilibrated my system in NVT, and then plot the potential energy.
> However the potential energy created with the two topology is not match.
> Thanks in advance,

MD is chaotic, and even identical topologies will yield different results.  If 
you want to test the equivalence of a topology, you should evaluate a 
single-point energy of an identical configuration of atoms with the two 
topologies.  That's the only meaningful test.




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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