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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