[gmx-users] swm4-ndp water with anisotropic polarizibility

Peter Hamm phamm at pci.uzh.ch
Tue Mar 11 12:27:34 CET 2014


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 

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 

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


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