[gmx-users] Output per-group kinetic energy

[Justin A. Lemkul]

Anthony Costa wrote:
>> Anthony Costa wrote:
>>> Dear All,
>>>
>>> I want to do something very simple: output, say, the kinetic energies
>>> for a subset of my system. For example some energy group of my system.
>>> Is this possible? Creating an index file, and listing each group as an
>>> energy group in my mdp file doesn't get this data into the energy
>>> file, only all the LJ, SR, etc., interactions are listed for each pair
>>> of groups.
>>>
>> See g_traj -ekt and/or -ekr.  Note that constraints are not considered, so the
>> raw result will not be correct.  Methods for re-calculating proper energies are
>> described in the list archive.
> 
> Thanks for your reply. I have searched the archive and have not found
> the information you're referring to. If it's simple, I would
> appreciate a reference.
> 

Searching for:

g_traj constraints

turns up tons of results, among which are a few useful ones:

http://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html
http://lists.gromacs.org/pipermail/gmx-users/2002-August/002244.html

Surely, with a bit more digging, you can find some directly related to kinetic 
energy.  I'm quite sure I've seen them, but a good deal of time has passed.

-Justin

> Best,
> Anthony
> 
>> -Justin
>>
>>> Cheers,
>>> Anthony

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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