[gmx-users] inclusion of water in gromacs input files

[Chetan Mahajan]

Hi,

I am new to gromacs and I used acpype (amber2gromacs) tool to generate
*.top and *.gro from Amber files *.prmtop and *.inpcrd. For  water, this
tool placed following in *.top file:


[ 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
1   3   1   0.09572   462750.4

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

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

[ system ]
 tio2_wpep

[ molecules ]
; Compound        nmols
 tio2_wpep        1
 NA+                  1
 WAT              3656

                                                                        *My
question is it does not include any topology details for 3656 water
molecules either in this file or separately. Instead it has topology
defined for standard water molecule in atoms section above. However,
Gromacs accepted these two files as they are and runs were made. Please
comment if I need to include water topology details for all 3656 water
molecules. *

Thanks
Chetan