[gmx-users] Interaction energy of system as a function of the interface area

[Justin Lemkul]

On 2/23/14, 3:51 AM, maryam haji wrote:
> Dear all
>
> My system consists of protein and CNT. I know I can calculate
> Interaction energy and interface area using g_energy and g_sas tools,
> respectively.
>
> I want to obtain Interaction energy of my system as a function of the
> interface area between the protein and CNT.
>
> How to do this?
>

If you already have time series of energies and interfacial areas, just plot one 
as a function of the other.  Using awk is your friend here, because you can 
easily parse the data from the Gromacs output files.  Now, whether or not the 
interaction energy is completely a function of interfacial area is another 
matter, but plotting it is simple.

-Justin

-- 
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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

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