[gmx-users] use of SW.itp...

[Dennis Sprous, PhD]

Dear All:

I am trying to make use of polarizable water models.

I have attempted to employ the Maaren & van der Spoel [2001.  JPC 
105:2618] model embodied by the sw.itp embedded in share/gromacs/top.  I 
encountered the following issues:

1.  the lines:

; [ defaults ]
; LJ    Geometric

where duplicated from my main *.top file.  Hence I commented these out.

2.  The atom types WO, WH, WS and WD were not in oplsaa, so I appended 
them to the file oplsaa.ff/ffnonbonded.itp.

3.  The atom WS (the shell atom) -- but not WD -- requires a mass to 
which I set to a minimal value in the itp file:

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
      1           WO       1    SM        OW1        1    1.24588     
15.99940
      2           WH       1    SM        HW2        1    0.62134      1.008
      3           WH       1    SM        HW3        1    0.62134      1.008
      4           WD       1    SM        DW        1     0.0          0.000
      5           WS       1    SM        SW        1    -2.48856     0.008

Before I start some MD, did I do anything against good practices here?

-- 
any problem          worth attack
proves its worth     by fighting back
                      Piet Heins "Grooks"

D.G. Sprous, PhD
BioLeap Inc.
Cambridge MA 02141