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

[dbiswal at ucalgary.ca]

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



thanks
Debasmita