Team:EPF-Lausanne/Information & references

Modeling reference

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.