From: Rachel Ruskin (
Date: Mon Apr 05 2010 - 12:02:44 CDT

Dear VMD experts,

I am using the NAMD Energy plugin to analyze a conformational change
of a protein. I created several protein morphs representing
intermediate conformations of this protein in between its initial and
final shape (through simple interpolation of coordinates), and then
ran MD on each of these configurations.

Here is where NAMD Energy comes in: I am interested in an energy
landscape of the conformational change--that is, the potential energy
difference between one protein morph and the next. I didn't have the
time or computational resources to do something like umbrella
sampling, so instead I hoped that NAMD energy might be useful, since
it can calculate the internal energy of a protein over several

However, the results I am getting for internal energy (that is,
selecting protein only) don't make much physical sense. The energy
difference between conformations is 2-3 orders of magnitude larger
than expected.

My questions:
Does the protein internal energy take into account the shielding from
the protein? (are two charges on opposite sides of the protein
shielded by the intervening charges?)
Am I missing some obvious reason NOT to use NAMD Energy for this calculation?
Additional, possibly off-topic question: should the protein-lipid
interaction energy and the protein-water interaction energy be
included in the potential energy landscape (if I'm interested in the
rate of transition over the potential energy barrier from one protein
conformation to another)

Thank you very much,

Rachel Ruskin
Amherst College, senior thesis student