[gmx-users] calculate torsional energy of the ligand from the trajectory

[Anton Feenstra]

David wrote:

> On Tue, 2005-05-03 at 16:42 +0200, Minami Mo wrote:
> 
>>Hi all,
>>
>>Does anyone know how to extract the torsional energy of (only) the
>>ligand from the MD simulation bounded to a protein? I have been
>>searching for it for some times but seem it was not asked before.
>>
>>My current idea is to extract the ligand in each frame to a pdb file,
>>and do the calculation. Any suggestion or tool that may serve this
>>purpose?
> 
> You can use mdrun -rerun in which you use a topology where all the
> protein dihedrals are taken away.

If you defined energy_groups in your mdp file, the info will already be 
in your energy file. If not, you'll need to add the energy_groups before 
doing the rerun.

(Unless you mean the rotational kinetic energy of the ligand, which is 
something else altogether, and AFAIK no Gromacs tool can calculate it 
right away.)

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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