Getting started with VMD and NAMD

VMD and NAMD are two closely linked molecular dynamics tools from the UIUC Computational Biophysics Group.  As you can probably guess from the ‘Biophysics’ header, the emphasis for this suite is on large-scale macromolecular clusters such as proteins or even lipid bilayers, meaning CHARMM and force field models are the order of the day.

Despite the emphasis on biochemistry, there is an interesting tutorial on simulating water permeation through carbon nanotubes.  When I stumbled across that tutorial on the same day I saw a post about desalinization using carbon nanotubes, I thought ‘kismet!’.

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How to add a feature to JChemPaint

In my last post, I provided instructions on how to compile an up to date version of JChemPaint.  While exciting … yeah, right … what you as the dabbling chemist / programmer really want to do is extend the functionality of JChemPaint.

As the boringest [sic] example I could come up with … let’s add a rotation tracker to the ‘2d rotate’ ability of JChemPaint, meaning when we rotate a molecule 90°, let’s add a display to the status bar so we know we’ve hit 90° exactly.

this is what we’ve got:

this is what we want:

but how the hell do we get there?

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