search

SENPAI-Molecular-Dynamics / SENPAI

Molecular dynamics simulation software
https://senpaimd.org
GNU General Public License v3.0
125 stars 16 forks source link

MOLV2000 format not entirely supported. #13

Closed JuhaJGamer closed 4 years ago

JuhaJGamer commented 4 years ago

Satanic molecules such as 

 OpenBabel10281909393D

 76 88  0  0  1  0  0  0  0  0999 V2000
    0.0000    0.0000   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000   -0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2 33  1  0  0  0  0
  3  4  1  0  0  0  0
  3 49  1  0  0  0  0
  3 50  1  0  0  0  0
  4  5  2  0  0  0  0
  4 34  1  0  0  0  0
  5 51  1  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  0  0  0  0
  6 46  1  0  0  0  0
  6 52  1  1  0  0  0
  7  8  2  0  0  0  0
  7 53  1  0  0  0  0
  8  9  1  0  0  0  0
  8 44  1  0  0  0  0
  9 10  1  0  0  0  0
  9 54  1  0  0  0  0
  9 55  1  0  0  0  0
 10 11  2  0  0  0  0
 10 47  1  0  0  0  0
 11 12  1  0  0  0  0
 11 56  1  0  0  0  0
 12 14  1  0  0  0  0
 12 13  2  0  0  0  0
 14 15  1  0  0  0  0
 14 57  1  0  0  0  0
 14 58  1  0  0  0  0
 15 16  2  0  0  0  0
 15 47  1  0  0  0  0
 16 17  1  0  0  0  0
 16 59  1  0  0  0  0
 17 18  2  0  0  0  0
 17 42  1  0  0  0  0
 18 60  1  0  0  0  0
 19 18  1  0  0  0  0
 19 20  1  0  0  0  0
 19 40  1  0  0  0  0
 19 61  1  1  0  0  0
 20 62  1  0  0  0  0
 20 63  1  0  0  0  0
 21 20  1  0  0  0  0
 21 22  1  0  0  0  0
 21 48  1  0  0  0  0
 21 64  1  1  0  0  0
 22 23  2  0  0  0  0
 22 65  1  0  0  0  0
 23 25  1  0  0  0  0
 23 24  2  0  0  0  0
 25 26  1  0  0  0  0
 25 66  1  0  0  0  0
 25 67  1  0  0  0  0
 26 27  2  0  0  0  0
 26 48  1  0  0  0  0
 27 28  1  0  0  0  0
 27 68  1  0  0  0  0
 28 29  2  0  0  0  0
 28 38  1  0  0  0  0
 29 69  1  0  0  0  0
 30 29  1  0  0  0  0
 30 31  1  0  0  0  0
 30 36  1  0  0  0  0
 30 70  1  1  0  0  0
 31 32  1  0  0  0  0
 31 71  1  0  0  0  0
 31 72  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 33 73  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 46  1  0  0  0  0
 36 37  1  0  0  0  0
 38 37  1  0  0  0  0
 38 39  1  0  0  0  0
 38 74  1  1  0  0  0
 39 40  2  0  0  0  0
 39 48  1  0  0  0  0
 40 41  1  0  0  0  0
 42 41  1  0  0  0  0
 42 43  1  0  0  0  0
 42 75  1  1  0  0  0
 43 44  2  0  0  0  0
 43 47  1  0  0  0  0
 44 45  1  0  0  0  0
 46 45  1  0  0  0  0
 46 76  1  1  0  0  0
M  END

Are immediately accepted with an atom count of 0 as seen 

Lowering potential energy to 10.000000 pJ...
+---------------------+
|         FILE        |
+---------------------+
Path...................satan3.mol
Name...................*****
Author................. OpenBabel10281909393D
Comment................ 76 88  0  0  1  0  0  0  0  0999 V2000
Atoms..................0
Bonds..................0

+---------------------+
|       UNIVERSE      |
+---------------------+
Duplicates to simulate.10
Atoms..................0
Temperature............273.000000 K
Pressure...............1.000000 hPa
Density................1.000000 g.cm-1
Total potential energy.0.000000 pJ
Universe size  ........0.000000 pm
Simulation time........1.000000 ns
Timestep...............1.000000 fs
Frameskip..............0
Iterations.............1000000

Simulation started
Simulation ended

<<< here

Note that this molecule is never supposed to have been created and will bring upon the end of worlds upon simulation start, as was prophesied thousands of years ago in ancient Sumeria.

Chelsea486MHz commented 4 years ago

"Pure" MOLV2000 won't work with SENPAI and is the main issue. The files have to be edited to include:

The issue lies in the fact your header isn't valid. Here is a corrected version:

Name
Author
Description
 76 88  0  0  1  0  0  0  0  0999 V2000
    0.0000    0.0000   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   ...

Additionally, even with a decent format and valid extra information, this system cannot be simulated. Since the atoms are at the same physical coordinates, an infinite potential will be evaluated and the simulation will fail.

It's a shame though, I was expecting a spectacular failure and explosion, but oh well.

JuhaJGamer commented 4 years ago

Damn, guess I can't summon satan today. Maybe another day I will find a way to create a spectacular explosion.