[gmx-users] Interaction energy between helices

[Natalia Alveal F.]

Dear Justin,

i do that you tell me, and when i do mdrun -rerun -deffnm new.tpr, there is
a error, because

Can not open file:
md-energy.xtc

Best regards!


2014-06-12 14:14 GMT-04:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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-- 
Natalia Alveal Fuentealba
Ingeniera en Bioinformática
Laboratory of Membranes Proteins Structure and Signalling
Departamento de Fisiología
Pontificia Universidad Católica de Chile
Alameda 340, Santiago, Chile
Fono: 56-2-3542877