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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