[gmx-developers] Potential energy calculation

Erik Lindahl lindahl at stanford.edu
Wed Feb 13 19:18:19 CET 2002

Vibin R wrote:

> Dear Sir
>         Can we calculate the potential energy of a structure from a
> pdbfile with gromacs, without doing either energy mininisation or MD. If
> it has to be done with slight adjustments in the source code, please let
> me know, where the changes has to be made. Basically i want to get the
> vanderwaals and coulombic interaction energies of a structure from a given
> pdb file.
>         Expecting your kind attention
> Regards
> vibin

Hi Vibin,

Together with Olivia Eriksson in Stockholm I've adapting things slightly to
be able to use gromacs in monte carlo and sidechain energy simulations. If
you want to try the CVS version of gromacs (that has monte carlo innerloops
without forces) you could use the attached somewhat documented wrapper
function to calculate the coulomb and lennard-jones energies directly. If all
parameters are in Gromacs units you'll get the energy in gromacs units too.

However, please note that a pdb structure can have an very high potential
energy unless you use the same forcefield as the structure was refined with.
Normally it's a good thing (TM) to do a few steps of energy minimization to
get around this, but your milage may vary.



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