[gmx-users] energy groups for specific parts of the molecule

[Justin Lemkul]

On 7/1/13 7:00 PM, Hovakim Grabski wrote:
> Dear Gromacs  users,
> I ran  a simulation between 6 molecules of Hypericin and  26 base pair long DNA, so for energy_grps I set HYP and DNA.
> Is there any way to get van der Waals and coulomb energy's of the interaction between hypericin and  a specific parts of  the DNA(phosphate groups for example)?
> Are there any tutorials?

Just make each molecule its own group and set those as your energygrps.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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

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