[gmx-users] Interaction energy between helices

[Justin Lemkul]

On 6/12/14, 2:02 PM, Natalia Alveal F. wrote:
> Thanks Justin, but for how long do this new simulation?

It's not a new simulation.  You're re-processing your existing trajectory. 
Usually the energy evaluations only take a few minutes.  The practical impact of 
energygrps during a run is usually fairly insignificant, but that's also a 
function of how many groups there are and how often you're writing to disk.

-Justin

> Natalia
>
>
> 2014-06-11 18:14 GMT-04:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 6/11/14, 5:36 PM, Natalia Alveal F. wrote:
>>
>>> Dear Gromacs users,
>>> I want to calculate the energy of interaction between two helices of a
>>> protein, but g_energy dont have the option for -ndx file to select these
>>> specific residues of a helix. How I can do this?
>>>
>>>
>> That's what energygrps in the .mdp file are for.  Re-calculate the
>> energies with mdrun -rerun using the new .tpr file.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================