Hydrogen molecule model

From: Mikhail Suyetin (msuyetin_at_gmail.com)
Date: Fri Oct 30 2009 - 10:42:19 CDT

Hello everybody,
I tried to perform simulation with hydrogen molecule, treated as
molecule consisting of three atoms:
two side atoms with no mass and charge q=0.468e and central atom
charged q=-0.936e and mass = 2H,
but I've got the following message:
-----------
Warning: Found 8192 H-H bonds.
FATAL ERROR: H atom 16441 bonded only to child H atoms
Stack Traceback:
  [0] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x409bda]
  [1] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x57085a]
  [2] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x574627]
  [3] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x57534e]
  [4] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x5820ec]
  [5] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x5bb042]
  [6] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x5bd8b8]
  [7] TclInvokeStringCommand+0x91 [0x6fa358]
  [8] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x714c3f]
  [9] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x6fad6b]
  [10] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x70123e]
  [11] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x7301a8]
  [12] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x7307eb]
  [13] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x7281f4]
  [14] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x5bd374]
  [15] /home2/ipmuran1/l1234567/./mvapich/namd2 [0x40c085]
  [16] __libc_start_main+0xf4 [0x37fc21d974]
  [17] _ZNSt19basic_ostringstreamIcSt11char_traitsIcESaIcEED1Ev+0x89 [0x4093a9]
Signal 15 received.
------------
If I change the mass of the central atom from 2H to 12.0, everything
working well.

Any approaches how to overcome this problem are welcome.

--
Sincerely yours,
Mikhail Suyetin

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