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

[Justin Lemkul]

On 5/23/13 11:27 AM, Bao Kai wrote:
> 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?
>

Your topology does not indicate any sort of shape constraints, nor should you be 
using any.

-Justin

> 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

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