[gmx-users] Shell dynamics with vdW terms.

Rafael Rodríguez Pappalardo rafapa at us.es
Tue Jun 9 09:51:13 CEST 2009


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.


Dr. Rafael R. Pappalardo
Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
e-mail: rafapa at us.es

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