Hi all,
I just noted that the tip3p water converted from amber format to gromacs
format is
[ 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 in amber99sb.ff/tip3p.itp. it is
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 it seems that the force_constants for O-H bond and H-O-H angle are
different? Does this mean amber and gromacs use different parameters for
tip3p water? or it's just acpype is not working right?
Thanks,
Yun
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