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

[Bao Kai]

Hi,

Thank you for your prompt reply.

I just think since we have added so many constraints on the shape of
the molecules, the molecules should keep their shapes.

I am wrong?  I have not done simulation with such big molecules
before.  I just did some simulations with water and CO2. The case can
be different, right?

Thanks,
Kai

On 5/23/13 11:16 AM, Bao Kai wrote:
> 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
>

I see nothing wrong.  The outcome seems totally normal for an MD
simulation.  If
molecules didn't change their configuration, what would be the point of
simulating? ;)

-Justin

>
>
> 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
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin