[gmx-users] Non-bonded energy

[Justin Lemkul]

On 6/7/16 12:23 AM, ABANTIKA PAL wrote:
> Hi,
>
> So, for calculating non-bonded energy, we have to consider all pair of atoms of the protein which are separated by a distance less than the cutoff distance. Please correct me if I am wrong.
>

That would indeed constitute the short-range nonbonded interactions within the 
protein.  But again, that number means nothing.

-Justin

> ----- Original Message -----
> From: "Justin Lemkul" <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Sent: Tuesday, June 7, 2016 6:50:32 AM
> Subject: Re: [gmx-users] Non-bonded energy
>
>
>
> On 6/6/16 9:00 AM, ABANTIKA PAL wrote:
>> Hi,
>>
>> I want to know which atoms are to be considered while calculating non-bonded energy of a protein. Whether it is all pair atom or there is a particular criteria while selecting the atoms.
>>
>
> The nonbonded energy of a protein would imply that any interactions within the
> defined cutoffs would be included.  Of course, such a quantity is not physically
> meaningful, but that's how it's calculated.
>
> -Justin
>

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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