[gmx-users] energy

[mirko busato]

Dear Justin,

Thank you very much for your quick reply,

In my .mdp file I set up energygrps to protein ITA. 
(ITA is the group for the Itaconic acid monomers)

After that I tried to launch g_energy command on .edr file. 

Is it right? 

which energy terms do you suggest me to use for my problem (to understand the affinity peptide-monomer)?


Thank you very much,


Mirko


On Friday, May 9, 2014 2:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 


On 5/9/14, 6:28 AM, mirko busato wrote:
> Dear Users,
>
> In my experiment, one petide of troponin protein  and many copies of the same type of  monomer, itaconic acid,(negatively charged) are assembled in a virtual box.
>
>
> I would like to understand , if there is a method to calculate the interaction energy between the peptide and the monomers.
>

That's what energygrps are for.

-Justin


> I am asking this because I would like to have an energetic value to determine the affinity of the itaconic acid monomer against the peptide.
>
> My system is in vacuum and  NA sodium ions weren't added to neutralize the system, so my system is charged.
>
> The force field used is CHARMM27  and I performed a minimization energy step  and an equilibration step.
>
>
> Could you help me?
>
> Thank you very much,
>
> Mirko
>

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

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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