AMBER Archive (2008)

Subject: RE: AMBER: POL3 with gaff and ff02EP

From: Ross Walker (
Date: Sun Jul 13 2008 - 23:40:02 CDT

Hi Grange,


The GAFF force field uses the standard AMBER equation and does not include
any polarization functions while FF02EP and POL3 include fluctuating
dipoles. Thus if you mix GAFF and FF02EP/POL3 you will have a very very
weird situation since there is no definition, and likely no support in the
code, to deal with the interaction between the dipoles of the polarizable
atoms and the lack of dipoles on the GAFF atoms. Likely what happens is
dipoles are included for all the atoms but the array locations containing
the polarizability terms for the GAFF atoms just contain junk, hence why it
ends up being unstable.


Gromacs should really quit with an error here telling you that such
simulations are not supported.


Short answer, don't mix polarizable and non-polarizable force fields in the
same simulation.


All the best



From: [] On Behalf Of
Grange Hermitage
Sent: Sunday, July 13, 2008 6:16 PM
Subject: AMBER: POL3 with gaff and ff02EP



Does anyone know why POL3 with gaff and ff02EP would lead to unstable
simulations but when POL3 is replaced with SPC (solvating with POL3BOX
replaced by solvating by SPCBOX) the simulation becomes stable?
I use amb2gmx to run the simulation on gromacs.


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