[gmx-users] Why the shape of the molecules changed?
Justin Lemkul
jalemkul at vt.edu
Thu May 23 17:19:43 CEST 2013
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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