[gmx-users] potential energy of a peptide in explicit DMSO

[Anton Feenstra]

Xiaoming Zhang wrote:

> Dear users,
> 
> I am running the MD simulation of a cyclic peptide in explicit DMSO. 
> It is straightforward to retrieve the potential energy of the whole
> system (peptide + DMSO) using g_energy.  However, I didn't find a way
> to calculate/retrieve the potential energy for the peptide only.  I
> was wondering if any of you had the experience and knew how to deal
> with it.

You need to define energy groups in your mdp file before you perform the 
simulation. Alternately, you can re-run your generated trajectory. See 
manual for more details.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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