[gmx-users] angle between benzene rings

[Justin Lemkul]

On 3/6/14, 6:14 PM, Sanku M wrote:
> Dear gromacs users
>   I would like to compute the angle of orientation between two benzene rings that I have simulated using gromacs.
> I think, for this, I have to get the vector normal to the plane of the benzene ring and then get the angle of among the unit vectors. Is there any tools in gromacs that can help me to do this? Does g_sgangle work here?

That's what g_sgangle -oa claims to do.  Have you tried it?

-Justin

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

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