Re: What is a good (small) test system for NAMD

From: Giacomo Fiorin (
Date: Tue Jul 10 2012 - 14:17:41 CDT

If you want to stick to two atoms, why not Na+ Cl-? :-)

On Tue, Jul 10, 2012 at 3:13 PM, Roy Fernando <> wrote:

> Dear All,
> I am looking for a small test system to test my TCL forces simulation.
> Ideal case is a two atom system. Can anyone of you suggest what is a good
> system for this purpose.
> I will be grateful if someone would like to share a pdb and psf files. I
> actually made a pdb and psf files by putting two Na ions in to a water box.
> But I could not equilibrate this system. System becomes unstable, when the
> velocities are applied after the minimizing at 0k temperature. A two atom
> system is subject to a Lenard Jones type potential and therefore the energy
> curve is known. That is why I am interested on two atom systems. Also it is
> the least complex system for testing an algorythm.
> What test systems you guys are using?
> I appreciate your suggestions.
> Regards,
> Roy

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