[gmx-users] Making Rigid Structure

[leafyoung81-group at yahoo.com]

--- 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.

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