[gmx-users] Shell dynamics with vdW terms.

Berk Hess gmx3 at hotmail.com
Tue Jun 9 10:02:47 CEST 2009


The equation you refer to is only an initial guess for the optimization.
The positions of the shells are optimized using the forces from
the full potential function.


> From: rafapa at us.es
> To: gmx-users at gromacs.org
> Date: Tue, 9 Jun 2009 09:51:13 +0200
> Subject: [gmx-users] Shell dynamics with vdW terms.
> Hello,
> I have some troubles understanding the way used by Gromacs in optimizing 
> the position of shells. In section 3.5.1 the manual says that the force on a 
> shell particle is decomposed into two terms. The first represents the 
> polarization and the second includes the Coulomb and van der Waals 
> interactions. It continues assuming that the second term is constant and 
> derives an analytic expression to calculate the shell position.
> My troubles arise after reading the paper: J. Phys. Chem. B 2009, 113, 
> 7270-7281 by A. Villa, B. Hess & H. Saint-Martin. In the paper they simulate 
> Lanthanides in water. In Table 2 they assign a 1/r**12 term to the ion-shell - 
> water-shell interaction (the A_MIM parameter). I believe that this term is 
> used in eq. 8 of the Supporting Information. Because is vdW like it seems to 
> me that it breaks the previously mentioned assumption of vdW constancy.
> Could anybody help me?
> Thanks a lot.
> Rafael
> -- 
> Dr. Rafael R. Pappalardo
> Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
> e-mail: rafapa at us.es
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