[gmx-users] Topology file and itp file

[Justin Lemkul]

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.

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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