[gmx-users] Vibrational, rotational and translational energy

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 6 18:33:46 CET 2017

On 06/02/17 17:59, qasimpars at gmail.com wrote:
> Dear users,
> Is that possible to calculate/get the vibrational, rotational and translational energy of a protein per residue with GROMACS?
> Total energy of a molecule physically consists of electronic, vibrational, rotational and translational parts. But GROMACS calculates only the bonded and non-bonded energies. How do the bonded and non-bonded energies represent the total energy of a system. I get confused :(
There is only total energy. Energy per residue has no physical meaning. 
However you can do a normal mode analysis of your protein and analyze 
the vibrational frequencies.

> Thanks in advance.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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