[gmx-users] Why the shape of the molecules changed?

[Bao Kai]

Hi, all,

I finally wrote a decane topology file. I used it to some simple simulation.

The energy minimization works, while after a simple nvt equilibration,
the shape of the molecules changed.

Please find the images before and after the nvt equilibration from the
following links.
https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png
https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png



The following is the topology part for the decane molecule.   Please
help to check if there is anything wrong.   C2 and C3 are CH2 and CH3
respectively.

[ defaults ]
; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ
    1          3          yes         0.5    0.5

[ atomtypes ]
;   type  at.num    mass    charge    ptype    sigma        epsilon
      C2   6     14.0270    0.0      A        0.374        0.4301
      C3   6     15.035      0.0      A        0.374        0.6243
[ moleculetype ]
; Name            nrexcl
D10                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1        C3      1    D10     1C3      1       0.0         15.035
 ; qtot -0.18
     2        C2      1    D10     1C2      2      0.0          14.027
  ; qtot -0.3
     3        C2      1    D10     2C2      3      0.0          14.027
  ; qtot -0.42
     4        C2      1    D10     3C2      4      0.0          14.027
  ; qtot -0.54
     5        C2      1    D10     4C2      5      0.0          14.027
  ; qtot -0.66
     6        C2      1    D10     5C2      6      0.0          14.027
  ; qtot -0.78
     7        C2      1    D10     6C2      7      0.0          14.027
  ; qtot -0.9
     8        C2      1    D10     7C2      8      0.0          14.027
  ; qtot -1.02
     9        C2      1    D10     8C2      9      0.0          14.027
  ; qtot -1.14
    10        C3      1    D10     2C3      10     0.0          15.035
  ; qtot -1.32


[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1  1.530000e-01  5430000  1.530000e-01  5430000
    2     3     1  1.530000e-01  5430000  1.530000e-01  5430000
    3     4     1  1.530000e-01  5430000  1.530000e-01  5430000
    4     5     1  1.530000e-01  5430000  1.530000e-01  5430000
    5     6     1  1.530000e-01  5430000  1.530000e-01  5430000
    6     7     1  1.530000e-01  5430000  1.530000e-01  5430000
    7     8     1  1.530000e-01  5430000  1.530000e-01  5430000
    8     9     1  1.530000e-01  5430000  1.530000e-01  5430000
    9    10     1  1.530000e-01  5430000  1.530000e-01  5430000

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     4     1
    2     5     1
    3     6     1
    4     7     1
    5     8     1
    6     9     1
    7    10     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    1     2     3     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    2     3     4     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    3     4     5     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    4     5     6     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    5     6     7     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    6     7     8     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    7     8     9     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02
    8     9    10     2  1.110000e+02  4.000000e+02  1.110000e+02  4.000000e+02

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    1     2     3     4     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00
    2     3     4     5     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00
    3     4     5     6     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00
    4     5     6     7     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00
    5     6     7     8     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00
    6     7     8     9     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00
    7     8     9    10     3  0.000000e+00 5.000000e+00  3.000000e+00
 0.000000e+00 5.000000e+00  3.000000e+00


[system]
sparkling water
[molecules]
D10 208

Thank you very much.

Best Regards,
Kai