[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly.

[Bao Kai]

Hi, all,

I am still working on the molecular simulation of CO2 and H2O mixture.

The information of the molecules types and the force field model are
all defined in the a.top file.

      1 [ defaults ]
      2 ; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ
      3     1          3          yes         0.5    0.5
      4 [ atomtypes ]
      5 ;   type  at.num    mass    charge    ptype    sigma        epsilon
      6       CO   6     12.0110    0.5888    A       0.27918       0.2398
      7       OC   8     15.9994   -0.2944    A       0.30000       0.6872
      8       OW   6     15.99940   -0.8476    A     0.316557     0.650194
      9       HW   1     1.00800    0.4238    A      0.00000       0.00000
     10 [ moleculetype ]
     11 ;name nrexcl
     12 CO2     3
     13 [atoms]
     14 ;   nr   type  resnr residue  atom   cgnr     charge       mass
........

     32 [moleculetype]
     33 ; molname nrexcl
     34 SOL 2
     35 [atoms]
     36 ;   nr   type  resnr residue  atom   cgnr     charge       mass
...............
     47 [system]
     48 sparkling water
     49 [molecules]
     50 CO2 100
     51 SOL              3000

I create on co2.gro file to put one CO2 molecule inside.

Then I used

genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top

to put 190 CO2 molecules inside the box.

Then I used
genbox -cp a.gro -o b.gro -box 7  -cs -maxsol 9810 -p a.top

to put 9810 H2O molecules inside the box.

In the file a.top, the No. of the H2O was updated correctly, while the
No. of the CO2 molecules was not updated.   The No. of the atoms in
.gro files are correct.

Can you please tell me the reason or how to solve it?

Thank you very much.

Best Retards,
Kai