[gmx-users] 1-4 interactions

[Liron Cohen]

I am using PME, can you elaborate about the decomposing you mentioned? 
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Wednesday, April 03, 2013 2:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 1-4 interactions

On 4/3/13 7:16 AM, Liron Cohen wrote:
> After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum everything (including the 1-4 interactions) or should I only include the SR interactions.

1-4 interactions are intramolecular and thus should not be included in
intermolecular energies.  If you're using PME, decomposing the long-range
component to the electrostatics term is challenging.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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