[gmx-users] 1-4 interactions

[Justin Lemkul]

On 4/3/13 7:49 AM, Liron Cohen wrote:
> I am using PME, can you elaborate about the decomposing you mentioned?

The mesh term includes all long-range interactions and is not broken down, even 
in the presence of energygrps in the .mdp file.  Some time ago, someone posted a 
method of several re-runs with custom .tpr files that suggested one could 
determine the individual contributions of different molecules to the mesh, but I 
don't know if anyone ever tried it or if it would even work.

People often measure these so-called "interaction energies," and they can be 
useful in some cases, but no force field has ever been parametrized to guarantee 
that such a number would even make sense.  Interaction energies may provide some 
qualitative insight, but if you want real quantitative metrics of interaction 
strength, you should probably be doing real free energy calculations.

-Justin

> ________________________________________
> 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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-- 
========================================

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

========================================