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

From: Aron Broom (
Date: Tue Jul 10 2012 - 14:23:47 CDT

If you want less strong forces than the Na+ Cl- system, try 2 argon atoms.
Also (although not strictly 2 atoms), you could do a 2 TIP3P water system
(although the PMF is more complex owing to geometry).

On Tue, Jul 10, 2012 at 3:17 PM, Giacomo Fiorin <>wrote:

> 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

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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