[gmx-users] calculate the dihed torsion energy

[Justin Lemkul]

On 7/12/16 6:54 AM, David van der Spoel wrote:
> On 12/07/16 10:12, 王珍 wrote:
>> Hi all,
>>     I want to calculate the dihed torsion energy(for example the dihed of
>> o3'-p-o5'-c5') using gromacs, how can i define the exergy_groups and how can I
>> extract the energy?
>> Thank you very much.
>>
> You can not in a simple manner. You would have to modify the topology to have
> all other torsions set to have zero parameters, and then do a zero step
> simulation (which will compute the energies ones but not integrate the positions).
>

And even then, the result is not useful.  The energy of the dihedral is simply 
calculated from the cosine series defined in ffbonded.itp.  If one includes 1-4 
interactions, that still does not give anything with physical meaning.  The 
conformational energy of the biomolecule (presumably DNA/RNA here) as a function 
of a given dihedral can be useful, if the force field was parametrized to yield 
a meaningful quantity (e.g. parametrized against QM relative conformational 
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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