[gmx-users] free energy and ions

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Thu Nov 28 12:23:31 CET 2002

Hi David

	Thank you for your words.

	My substrate has charge +1 and protein +6, so complex has +7.  I'm
using then CL- as counterions.  Such value of charge is low enough for
	I'll check for Born corrections.  Thanks again.

On 27 Nov 2002, David wrote:

> On Wed, 2002-11-27 at 20:04, Alan Wilter Sousa da Silva wrote:

> There is no easy answer for this question... Ideally you'd want to have
> real equilibrium distributions of ions. However you apparently don't see
> that on the ns timescale. If you leave out the ions you also have a
> problem. You didn't state the charges on substrate and ligand, but if
> they are low you maybe could get away with a cut-off and maybe an
> analytical correction to the energy. Check the literature for Born
> correction.

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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