[gmx-users] Potential energy of the prot. only
feenstra at chem.vu.nl
Mon Jul 26 17:52:23 CEST 2004
pascal.baillod at epfl.ch wrote:
> I am trying to compute the potential energy of the protein of my system
> simulated in explicit spc water. I have the energy groups protein and other and
> am trying to figure out whcih terms of the g_energy output I should sum up to
> get the proteins total potential energy (without interactions with the solvent).
> To me the terms 1 4 3 4 46 47 48 0 make most sense and give the result here
> below for the trpc (a 20 residue peptide in a half folded conformation). I
> assume term 49 (49=Coul-14:Protein-Protein) is already counted in term 46
> (=Coul-SR:Protein-Protein) and 48 (=Coul-LR:Protein-Protein). Similarily, 50 is
> already counted in 47, I suppose..
No, to get all coulombic interaction energies within the protein,
you have to add 46, 48 and 49 (i.e., all 'Coul-*:Protein-Protein'
energy groups), and for LJ: add 47 and 50.
It would be nice if you could tell g_energy that you want all '*:Protein-Protein'
groups. Anyone'd care to implement that?
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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