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Team:EPF-Lausanne/Implementation
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===Run a complete simulation=== | ===Run a complete simulation=== | ||
We start from .pdb, .psf, .rtf generated in the previous section. Complete process is on a separate page [[Team:EPF-Lausanne/Modeling/RunSimulation|How to run a simulation]]. | We start from .pdb, .psf, .rtf generated in the previous section. Complete process is on a separate page [[Team:EPF-Lausanne/Modeling/RunSimulation|How to run a simulation]]. | ||
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Revision as of 10:11, 27 July 2009
Contents |
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, and proceed to mediate activation of an attached kinase domain.
Generating input files
First we need a compatible .pdb in addition to parameter and topology files. 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.
.conf parameters
We should explain here what are the keywords we use in the .conf.
Run a complete simulation
We start from .pdb, .psf, .rtf generated in the previous section. Complete process is on a separate page How to run a simulation.
