[gmx-users] Problem in Energy minimisation for a rigid body system

[Mark Abraham]

dbiswal at ucalgary.ca wrote:
> Hi,
> 
> I want to do a rigid body simulation for a 7-site model system, where the
> center is occupied by a metal ion and the 6 octahedral sites are occupied
> by 6 dummy atoms. Initially I tried to simulate a 5-site square planar
> rigid body system, where the center is occupied by the metal atom and four
> dummy atoms in the 4 corners of square plane. I could successfully
> equilibrate my system and proceed with my simulation. While trying to make
> my 5-site model, a rigid body, I constrained a bunch of distances between
> atoms by using the option "constraints = all-bonds" option in the .mdp
> file and also defining a bunch of improper dihedrals in .itp file. It
> worked perfectly and later I wanted to shift to my 7-site model. So in my
> old 5-site model, I just added another 2 dummy atoms, one above and
> another below the square plane. I tried to make it rigid by constraining
> another bunch of distances, the same way as I did it before. However, I'm
> not able to perform energy minimization, during which I receive LINCS
> WARNING messages. Can you please suggest me, where am I going wrong ? I'm
> pasting below  the atoms and bonds directive of .itp file.
> 
> [ atoms ]
> ;   nr   type   resnr   residu   atom  cgnr   charge   mass
> 1        M1       1      SET      M     1     0.0       53.380
> 2        DZ1      1      SET      D1    1     0.5       3.000
> 3        DZ2      1      SET      D2    1     0.5       3.000
> 4        DZ3      1      SET      D3    1     0.5       3.000
> 5        DZ4      1      SET      D4    1     0.5       3.000
> 6        DZ5      1      SET      D5    1    -0.5       3.000
> 7        DZ6      1      SET      D6    1     0.5       3.000
> 
> [ bonds ]
> ;  ai  aj  funct   dist       kb
> 1      2     1     0.06000    267520.0
> 1      3     1     0.06000    267520.0
> 1      4     1     0.06000    267520.0
> 1      5     1     0.06000    267520.0
> 2      3     1     0.08485    267520.0
> 3      4     1     0.08485    267520.0
> 4      5     1     0.08485    267520.0
> 2      5     1     0.08485    267520.0
> 1      6     1     0.02000    267520.0
> 1      7     1     0.02000    267520.0
> 2      6     1     0.06324    267520.0
> 3      6     1     0.06324    267520.0
> 4      6     1     0.06324    267520.0
> 2      7     1     0.06324    267520.0
> 3      7     1     0.06324    267520.0

If the symmetry of the system is to be octahedral, then you should try 
defining a symmetric set of bonds. You've omitted 5-6, 4-7 and 5-7.

Mark