Re: Hydrogen molecule model

From: Axel Kohlmeyer (
Date: Fri Oct 30 2009 - 15:00:12 CDT

On Fri, 2009-10-30 at 18:42 +0300, Mikhail Suyetin wrote:
> Hello everybody,

hi mikhail,

> 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,

apart from the fact that you are throwing off NAMD's heuristics
in a bad way, you simply cannot simulate a "molecule" like this
in classical MD. without any mass on atoms there is no way to
integrate the integrate the equations of motion. you can only
have massless particles as pseudo particles or virtual sites,
where their position is derived from other coordinates and the
resulting forces are translated back to the original sites.


Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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