[gmx-users] Implicit solvent models in Gromacs ?

Marc Baaden baaden at smplinux.de
Wed Dec 12 00:57:39 CET 2001


I was wondering wether anyone has ever used any type of implicit solvent model
with Gromacs, however simple or complicated, and what their experiences were.

As far as i could understand from the manual, e.g. a simple model like a distance
dependent dielectric is not easily possible (not with standard mdp options).

How difficult would it be to implement a user defined function for the dielectric ?

I suppose the most universal  (not limited to the dielectric) approach would be
to plug in an additional force calculation routine somewhere in mdrun. Has
anybody ever done so and is there some available code for this ?

My purpose - at the moment - is that I want to run some cheap and quick test
calculations "in vacuo" but with periodic boundary conditions, and some kind
of (dielectric, ..) damping to stop my system from falling apart (which it does
if I just use an in vacuo approach).

Thank you in advance,

  Marc Baaden

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