[gmx-users] The small organic molecule occurred deformation during simulation

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================