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 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed])

VMD informations

VMD is used to visualize molecules. It is quite user friendly.

• A tutorial for VMD can be found [http://www.ks.uiuc.edu/Training/Tutorials/ here].

NAMD informations

NAMD performs minimization and equilibration.

• A tutorial is on the same page as for VMD, [http://www.ks.uiuc.edu/Training/Tutorials/ here].
• [http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/ 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.

• [http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/ Building Gramicidin A: Equilibration]: protocol uses a single .conf file, heating process is too fast.
• [http://www.biochemistry.uab.edu/robinson/documents/howto/modeling/NAMD_notes.htm NAMD notes from Robinson Lab]: a really nice heating process, but involves different .conf files, which is really painful.