[gmx-users] Making Rigid Structure

[X.Periole]

On Mon, 13 Jun 2005 00:04:42 -0700 (PDT)
  <leafyoung81-group at yahoo.com> wrote:
> 
> 
> --- Yang Ye <leafyoung at yahoo.com> wrote:
> Hi, 
> 
> I was setting up a system consisting a structure of
> points. All points should be fixed relatively to
> each
> other. I was trying to use bonds, angles and
> exclusions in the molucular definition but MD runs
> revealed that the structure turned to other "stable"
> forms.
> 

1) may be you want to use constrains on your bonds.
2) the kb you use is small. check the topology to get
an order of magnitude.

XAvier
> My itp is
> 
> [ moleculetype ]
> ;name  nrexcl
> Mol  4
> 
> [ atoms ]
> ;nr  type   resnr   residu  atom    cgnr   charge   
> 
>  mass  
>  1  S      1       MOL     S1      1       1.0     
> 
>  12.5
>  2  S      1       MOL     S14     2       1.0     
> 
>  12.5
>  3  S      1       MOL     S26     3       1.0     
> 
>  12.5
> 
> [ bonds ]
> ;  ai   aj   funct       b0     kb
>    1    2    1   11.000    1e00 ; (0,1)
>    1    3    1    7.778    1e00 ; (0,2)
>    2    3    1    7.778    1e00 ; (1,2)
> 
> [ angles ]
> ;  ai   aj   ak   funct    theta     the0
> ;    1    2    3    1   45.000    1e00 ; (0-1-2)
> ;    1    3    2    1   90.000    1e00 ; (0-2-1)
> ;    2    1    3    1   45.000    1e00 ; (1-0-2)
> 
> ;[ pairs ]
> ;  ai   aj  funct       c6    c12  
> ;    1    2      1      0e0    0e0 ; (0,1)
> ;    1    3      1      0e0    0e0 ; (0,2)
> ;    2    3      1      0e0    0e0 ; (1,2)
> 
> [exclusions]
>  1   2   3    
>  2   3   
> 
> Yang Ye
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