[gmx-users] different tip3p water parameters between AMBER and GROMACS

[Yun Shi]

Hi all,

I found that the 99SB force field in AMBERTOOLS1.5 and GROMACS4.5.4 have
different force constants for bond and angle parameters, after converting
them to the same unit.

So for those in AMBER
[ moleculetype ]
; molname       nrexcl ; TIP3P model
  WAT             2

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge       mass
     1     OW      1     WAT     O      1     -0.834   16.00000
     2     HW      1     WAT    H1      1      0.417    1.00800
     3     HW      1     WAT    H2      1      0.417    1.00800

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572   462750.4 0.09572   462750.4
1   3   1   0.09572   462750.4 0.09572   462750.4

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   104.520    836.800  104.520    836.800
#else
[ settles ]
; i j   funct   length
1   1   0.09572 0.15139

[ exclusions ]
1   2   3
2   1   3
3   1   2
#endif






while for GROMACS, that is, in the amber99sb.ff/tip3p.itp file,

[ moleculetype ]
; molname       nrexcl
SOL             2

[ atoms ]
; id  at type     res nr  res name  at name  cg nr  charge    mass
  1   OW          1       SOL       OW       1      -0.834    16.00000
  2   HW          1       SOL       HW1      1       0.417     1.00800
  3   HW          1       SOL       HW2      1       0.417     1.00800

#ifndef FLEXIBLE

[ settles ]
; OW    funct   doh     dhh
1       1       0.09572 0.15139

[ exclusions ]
1       2       3
2       1       3
3       1       2

#else

[ bonds ]
; i     j       funct   length  force_constant
1       2       1       0.09572 502416.0   0.09572        502416.0
1       3       1       0.09572 502416.0   0.09572        502416.0


[ angles ]
; i     j       k       funct   angle   force_constant
2       1       3       1       104.52  628.02      104.52  628.02

#endif



So I wonder why different parameters for tip3p water are used in GMX, even
for the save force field ?

Thanks for any suggestion,

Yun
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