[gmx-users] The small organic molecule occurred deformation during simulation
jalemkul at vt.edu
Sun Aug 6 02:37:26 CEST 2017
On 8/4/17 4:42 AM, yujie liu wrote:
> Hello, users
> I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as phenol. I want to know whether the situation is normal? In addition, I employed gromos54a7.ff
Slight out-of-plane distortions are possible because the rings aren't fully
rigid. But if you're seeing significant distortion, it suggests your topology
is wrong, likely due to missing or incorrect improper dihedrals, which serve to
prevent out-of-plane deformation.
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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