How to incorporate 3 site hydrogen molecule

Dear all,

Please tell me how to incorporate 3 site hydrogen molecule inside a
cage compound.

Thank you,

See the doc page for the read_data command. You
have to list the bonds/angles of your individual molecule(s).


thanks steve

As far as I know, the problem is more complicated. In 3-site hydrogen model point charges are placed at the hydrogen nuclei and at the center of mass of the hydrogen molecule (something like TIP4P water). The simplest way to construct such molecule is:

  1. define two hydrogen atoms with corresponding mass, charge and LJ parameters

  2. put virtual atom between them at the center of molecule (this atom must have very small mass, zero LJ parameters and non-zero charge)

  3. constrain bonds/angles by fix shake or fix rigid command

I’m not sure that such model would work correctly, may be you need to write a new pair style.

Grigory Smirnov

2012/3/19 SUKANTA MONDAL <sukanta.mail13@…36…24…>

thank you very much Grigory.

With best regards,