Re: Packaging 100 cations and anions in a box

From: Joshua D. Moore (
Date: Wed Dec 07 2005 - 02:25:23 CST

I use Vega ZZ to build most of my simulations.

You can build a single cation/anion pair and then replicate it using this
program. What is useful is that it will write out the necessary .psf and
.pdb files that you need as NAMD input. This takes a little work with
Vega ZZ as you have to build a pdb FAT formatted file including all of the
connections and charge information (from your force field). The manual has
a nice description of this, and you only really have to do it once per
molecule you are studying.


On Tue, December 6, 2005 11:47 pm, wrote:
> Hi,
> I am a beginner in NAMD. For my project I need to create a model for
> simulation in NAMD with 100 cations and anions packed in a cubic box. Is
> there
> a script that would package the atoms in the box. I am not sure how to go
> about with this.
> Anybody please help.
> Thank you,
> Indu.

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