[gmx-users] gromacs bond energy calculate

[Justin Lemkul]

On 5/25/17 3:57 AM, 王珍 wrote:
> Hi all,
>     Recently i want to cauculate the bond energy and angle energy for my RNA system, and the RNA was simulated by gromacs about 100 ns, could I use the command of gromacs to calculate the bond energy and angle energy for the RNA residues in my all-atom molecular dynamics simulation? Thank you very much!

Use convert-tpr to create a subset .tpr file that contains only RNA, and use 
trjconv to create a trajectory that contains only RNA.  Then supply those files 
to mdrun -rerun to recalculate the energies.

-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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