Implementation of the simulation

LOV domains are the light-sensitive portion of phototropins. They absorb light through a flavin cofactor, photo-chemicaly form a covalent bond between the chromophore and a cysteine residue in the protein.

Generating input files

In this section, we explain all the steps to create needed files for namd, except the .conf file. We need a compatible .pdb in addition to parameter and topology files to go through. Steps to generate all the input files are explained in detail on this page How to generate input files. This is a kind of summary of the tuto.

Namd .conf parameters

Namd can run different kind of simulations, from minimization to MD. Here are the .conf we use. NamdConf

Launch a simulation

We start from .pdb, .psf, .rtf generated in the previous section and we explain how to launch namd on both clusters we have access to. Complete process is on a separate page How to launch a simulation.