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Team:EPF-Lausanne/Information & references
From 2009.igem.org
LOVTAP simulation
We will follow the following article protocol:
Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, 91, 3630-3639, 2006 (Pubmed)
VMD informations
VMD is used to visualize molecules. It is quite user friendly.
- A tutorial for VMD can be found here.
NAMD informations
NAMD performs minimization and equilibration.
- A tutorial is on the same page as for VMD, here.
- NAMD 2.7b1 User's Guide
- Summary of parameters setting
Run a simulation
A simulation is composed of different steps. Here are a few links that deal with heating and stabilization.
- Building Gramicidin A: Equilibration: protocol uses a single .conf file, heating process is too fast.
- NAMD notes from Robinson Lab: a really nice heating process, but involves different .conf files, which is really painful.
