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

[Bao Kai]

Hi, Justin,

Thank you for your reply.

It is a little weird and inconvienient that genbox does not update the No.
of solute molecules.  Is it designed in this way? Does it have any reason
for that?

For my case, the  inear, 3-atom model of CO2 works pretty well. I got the
model from a paper from Zhenhao Duan.   I guess I will use this model for
the project before I get something wrong.

Best Regards,
Kai



> ------------------------------
>
> Message: 5
> Date: Thu, 04 Oct 2012 17:34:22 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] The No. of the CO2 melecules in top file can
>         not     be updated correctly.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <506E00DE.9050505 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 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
>
> --
> ========================================
>
> 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
>
> ========================================
>