[gmx-users] excluding electrostatic interactions

[Mark Abraham]

On 4/05/2011 8:08 AM, Sikandar Mashayak wrote:
> yeah, it says PME cant be excluded using energy exclusion, so I am 
> wondering about any other way to exclude it?

There is none.

One option is to run the simulation with PME for the improved sampling 
accuracy, and then to use mdrun -rerun  with some other electrostatics 
method if you really think these forcefields' non-bonded interactions 
can be decompose groupwise and end up meaning something.

There was an approach posted in the last month or two that does multiple 
reruns with PME to achieve the same effect.

Mark

> On Tue, May 3, 2011 at 5:01 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Sikandar Mashayak wrote:
>
>         Hi
>
>         I want to compute only the non-bonded ( LJ + EL) interactions
>         between Protein and Solvent and exclude non-bonded
>         interactions between Protein Protein & SOL SOL.
>         But energy exclusion group does not necessarily exclude the
>         non-bonded electrostatic interactions while using PME option
>         for coulombtype.
>         So I am just wondering if I were to compute electrostatic
>         interactions between just Protein SOL with PME, how can I do that?
>
>
>     Hasn't this already been answered?
>
>     http://lists.gromacs.org/pipermail/gmx-users/2011-April/060594.html
>
>     -Justin
>
>         thanks
>         sikandar
>
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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