[gmx-users] constraints using all-angles

[Sang-Won Park]

Hello,

I'm trying to do set a configuration for BMIM PF6 with rigid body anion.
So, I tested all-angles constraints for one molecule of PF6-.

Below is the conf.gro file.
-----------------------------------------------------
PF6
    7
    1PF6     P1    1   0.000   0.000   0.000
    1PF6     F1    2   0.156   0.000   0.000
    1PF6     F2    3   0.000   0.156   0.000
    1PF6     F3    4   0.000   0.000   0.156
    1PF6     F4    5  -0.156   0.000   0.000
    1PF6     F5    6   0.000  -0.156   0.000
    1PF6     F6    7   0.000   0.000  -0.156
   2.50000   2.50000   2.50000

-----------------------------------------------------

And below is a part of .top file. I fix all bonds and the distances
between fluorine atoms.
-----------------------------------------------------
[ moleculetype ]
; Name            nrexcl
PF6                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1         P1      1    PF6     P1      1       1.34    30.9738
     2         F1      1    PF6     F1      1      -0.39   
     3         F2      1    PF6     F2      1      -0.39   
     4         F3      1    PF6     F3      1      -0.39   
     5         F4      1    PF6     F4      1      -0.39   
     6         F5      1    PF6     F5      1      -0.39   
     7         F6      1    PF6     F6      1      -0.39   

[ constraints ]
;  ai    aj funct       b0
    1     2     1   0.1560	; bond length = 0.1560 nm
    1     3     1   0.1560
    1     4     1   0.1560
    1     5     1   0.1560
    1     6     1   0.1560
    1     7     1   0.1560
    2     3     2   0.22061731573	; sqrt(2)*0.1560 nm
    4     5     2   0.22061731573
    6     7     2   0.22061731573
    3     4     2   0.22061731573
    5     6     2   0.22061731573
    2     7     2   0.22061731573
    2     4     2   0.22061731573
    2     6     2   0.22061731573
    3     5     2   0.22061731573
    3     7     2   0.22061731573
    4     6     2   0.22061731573
    5     7     2   0.22061731573
    2     5     2   0.3120	; 2*0.1560 nm
    3     6     2   0.3120
    4     7     2   0.3120
------------------------------------------------------------------
After minimizing the configuration, I got the confout.gro file as
follows.
------------------------------------------------------------------
PF6
    7
    1PF6     P1    1   0.000   0.000   0.000
    1PF6     F1    2-592.510   0.000   0.000
    1PF6     F2    3   0.000-592.510   0.000
    1PF6     F3    4   0.000   0.000-592.510
    1PF6     F4    5 592.510   0.000   0.000
    1PF6     F5    6   0.000 592.510   0.000
    1PF6     F6    7   0.000   0.000 592.510
   2.50000   2.50000   2.50000

------------------------------------------------------------------

When I ran a simulation with md integrator option, it shows several
messages as follows, and finally all the atoms go to infinity.

------------------------------------------------------------------
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 105.918804, max 105.972168 (between atoms 1 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      2  180.0    0.1560  16.6815      0.1560
      1      3  180.0    0.1560  16.6710      0.1560
      1      4  180.0    0.1560  16.6800      0.1560
      1      5  180.0    0.1560  16.6772      0.1560
      1      6  180.0    0.1560  16.6877      0.1560
      1      7  180.0    0.1560  16.6787      0.1560
      2      3  180.0    0.2206  23.5848      0.2206
      4      5  180.0    0.2206  23.5873      0.2206
      6      7  180.0    0.2206  23.5923      0.2206
      3      4  180.0    0.2206  23.5840      0.2206
      5      6    nan    0.2206  23.5915      0.2206
      2      7  180.0    0.2206  23.5890      0.2206
      2      4  180.0    0.2206  23.5897      0.2206
      2      6  180.0    0.2206  23.5939      0.2206
      3      5  180.0    0.2206  23.5824      0.2206
      3      7  180.0    0.2206  23.5832      0.2206
      4      6  180.0    0.2206  23.5931      0.2206
      5      7  180.0    0.2206  23.5866      0.2206
Wrote pdb files with previous and current coordinates
------------------------------------------------------------------

What's wrong with my input files?