[gmx-users] Bond rotation freedom or mobility

[Justin Lemkul]

On 8/25/15 2:31 PM, Eric Smoll wrote:
> Hello GROMACS users,
>
> I am interested in quantifying the freedom or mobility of specific
> carbon-carbon single bonds in a organic molecule. Does anyone know the most
> appropriate method to do this? Can I make use of "gmx chi"?
>

No, gmx chi is specific for proteins (a lot of hard-coded atom names).  If you 
just want rotation about various bonds, that's just a dihedral rotation and 
therefore easily handled with gmx angle (you can even count number of 
transitions, etc).

-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 629
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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