[gmx-users] SiO2 simulation again.

[Mehmet Suezen]

Hi,

Try to devide Silicons and oxygens in to two different [ moleculetype ].
And order particles in gro file respectively. (Not randomly, it will not
work:-)

cheers,
mehmet


Lianqing Zheng wrote:
> 
> Dear All:
> 
> I am trying to simulate an all-atom (no bonded interaction) system of SiO2
> with Coulomb and Buckingham potentials. The following are the .top and
> .gro files that I constructed. Do you know if there is any error or flaw
> in them? When I ran mdrun, I got an error of "Arithmetic Exception (core
> dumped)." Though it could be many reasons, I don't know if I made the
> format of top and gro files right with the system. Could you take a
> minute to check them?
> 
> ;topology file
> [ defaults ]
> 2 1
> [ atomtypes ]
> ;name        mass      charge   ptype            c6           c12
>     O    15.99940       -1.20        A          0.0 0.0 0.0
>    SI    28.08000        2.40        A          0.0 0.0 0.0
> [ nonbond_params ]
>   ; i    j func           a             b       c6
>     O    O    2 1.339973E+5          27.6       1.688507E-2
>     O   SI    2 1.737112E+6       48.7318       1.288457E-2
>    SI   SI    2         0.0           0.0       0.0
> [ moleculetype ]
> SI 0
> [ atoms ]
> 1       SI      1       SI      SI      1       2.4     28.08000
> [ moleculetype ]
> O 0
> [ atoms ]
> 1       O       1       O       O       2       -1.2    15.99940
> [ system ]
> Silica SiO2
> [ molecules ]
> SI 512
> O 1024
> ; End of top file
> __________________________
> gro file:
> 1536
>     1    O    O    1  -0.717  -1.254  -1.254 -1.3797 -0.5947 -1.0028
>     1   SI   SI    2  -1.344  -1.344  -1.344  0.7731 -0.8680  0.4347
>     2   SI   SI    3  -0.985  -0.985  -1.344  0.1876  1.1196  1.3407
>     2    O    O    4  -1.075  -0.896  -1.254  2.4244  1.3673  3.6743
>     3    O    O    5  -0.896  -1.075  -1.254 -1.3595 -1.2375 -1.6633
>     3   SI   SI    6  -0.985  -1.344  -0.985  1.6699 -1.3636 -0.0800
>     4    O    O    7  -1.075  -1.254  -0.896  2.3342 -3.2442  0.3516
> ....
>  1023    O    O 1534   1.254   1.254   1.433  0.0548  0.6022  4.3814
>   512   SI   SI 1535   1.344   1.344   1.344 -1.3755  1.1702 -0.9112
>  1024    O    O 1536   1.433   1.433   1.433 -2.6078 -1.6520  0.2689
> 2.866400 2.866400 2.866400
> (End of gro file)
> 
> When using grompp to get .tpr file, I got a warning:
> 
> Warning: atom names in fs.top and fs.gro don't match (SI - O)
> (more than 20 non-matching atom names)
> Warning 1 [file "fs.top", line 32]:
>   682 non-matching atom names
>   atom names from fs.top will be used
>   atom names from fs.gro will be ingnored
> 
> Actually, for the most simple all-atom systems, such as liquid argon, how
> do we deal with those directives such as [molecules]? I think these two
> systems are similar in the view of file format.
> 
> I'd appreciate for your great help!
> 
> Lianqing
> 
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