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

[Justin Lemkul]

On 10/4/12 5:29 PM, Bao Kai wrote:
> 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?
>

genbox only updates water molecules in the topology.  Anything else is up to 
you.  Beware that a linear, 3-atom model of CO2 is probably not going to work 
due to issues with linear angles, as has been discussed frequently on the list. 
  A more robust approach involves virtual sites.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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