[gmx-users] Thole polarization between different molecules

[David van der Spoel]

On 2012-08-02 16:01, avilaverde wrote:
> Hi,
>
> 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+)?
>
This is not possible in the current code.

> 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
> direction?
>
> Thank you,
>
> Ana
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Thole-polarization-between-different-molecules-tp4999928.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se