[gmx-users] Thole polarization between different molecules

avilaverde avilaverde at fisica.uminho.pt
Thu Aug 2 16:01:10 CEST 2012


I'm interested in using models that require Thole polarization in Gromacs
but I'm having trouble understanding the syntax of the [thole_polarization]
entry because it is not yet explained in the manual.  I've looked online for
examples but could not find any that applied to the case I am interested in. 
Can someone send me an example file where this parameter is used in a
simulation containing more than one type of molecule (e.g. water and Mg2+)?

I found one example on the Gromacs lists
(http://lists.gromacs.org/pipermail/gmx-developers/2006-March/001571.html) :
;[ thole_polarization ]
;dipole 1    dipole 2
;at1   at2    at1   at2    func  const   pol dip 1           pol dip 2
1 5 6 9 2 2.6 0.001237576 0.001217571

The problem is that in this example I can only specify Thole
polarization-type interactions between atoms belonging to the same molecule
because these interactions are described by atom id, not atom type (I tried
using atom types, without success).  Can anyone point me in the right

Thank you,


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