[gmx-users] free energy and ions

[Alan Wilter Sousa da Silva]

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
cut-off?
	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