Thanks, Justin, for the quick response. Yes, I can see what to change
in gmxlib/bondfree.c
Best wishes
Peter
On 3/11/14, 7:27 AM, Peter Hamm wrote:
Hi
I'm trying to set up a slightly modified version of swm4-ndp water with
anisotropic polarizibility. In contrast to sw-water, where the Drude
(shell)
particle is connected to a dummy particle, it is connected to the
oxygen in
swm4-ndp. In sw.itp, ananisotropic polarizibility is defined by:
[ water_polarization ]
; See notes above. Alphas in nm^3 (See ref. above)
; O H H D S funct al_x al_y al_z rOH rHH rOD
1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139
0.0137408
I guess, the "4 5" means that the Drude particle (5) is connected to
the dummy
particle (4). I therefore changed it to
[ water_polarization ]
O H H D S funct al_x al_y al_z rOH rHH rOD
1 2 3 1 5 1 0.0010583 0.0011435 0.0010975 0.09572 0.15139
0.0257788
so that Drude particle (5) is now connected to the oxygen (1). This
however
generates a warning in grompp:
"WARNING 1 [file swm4-ndp-mod.top, line 33]: Duplicate atom index (1) in
water_polarization"
You've repeated atom number 1, which the code is interpreting as both
a Drude and the oxygen atom.
My question: Is [ water_polarization ] specific for sw-water with the
shell
particle necessarily connected to the dummy particle, or, can I
ignore the
warning, or, is there another syntax to do what I want to do (i
couldn't find
any real description of the syntax of [ water_polarization ]).
Best wishes, and thanks in advance for any help you can offer
The topology format and the code itself for water polarization is
specific to the setup of the SW model. I have been working on
generalizing the shell/Drude code for a while now, and the
introduction of general anisotropy is not difficult to do, though my
implementation is largely untested and therefore not suitable for the
public just yet. The code in gmxlib/bondfree.c (water_pol function)
can be easily modified.
-Justin
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