[gmx-users] Lenard Jones interaction between two chains

[Justin Lemkul]

On 6/10/17 12:36 PM, Simon Kit Sang Chu wrote:
> Hi,
> 
> I am working on a protein dimer. Since they are not linked by a bond, after
> pdb2gmx two topology files are produced. Each of them contains all atoms in
> their individual chains and their respective posre.itp contains information
> of position restraint.
> 
> However, after looking into the topology files, I only see pair interaction
> within the chain itself. May I ask natively - where is the inter-chain
> Lenard Jones interaction written?
> 

Pairs are 1-4 interactions and therefore are intramolecular.  There are no 
explicit lists of intermolecular interactions as these are dynamic as the system 
trajectory evolves.

-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 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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