[gmx-users] Potential energy of a single amino acid residu

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 10 18:26:38 CET 2009

Tom Venken wrote:

> Mu-Z              Coul-SR:r_8-r_8   LJ-SR:r_8-r_8     LJ-LR:r_8-r_8
> Coul-14:r_8-r_8   LJ-14:r_8-r_8     Coul-SR:r_8-rest  LJ-SR:r_8-rest
> LJ-LR:r_8-rest    Coul-14:r_8-rest  LJ-14:r_8-rest    Coul-SR:rest-rest
> LJ-SR:rest-rest   LJ-LR:rest-rest   Coul-14:rest-rest LJ-14:rest-rest

The rest of the protein has to be one of your energy groups, otherwise the only 
groups are r8 and everything else in your system.

Once you've done that you'll see terms like Coul-SR:r_8-Protein_&_!r_8 (or 
something like that), as long as your index groups are set up correctly.



Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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