Felipe Villanelo wrote:
Hi guys, i'm working on binding energy of two proteins. I will try to
use thermidynamic integration, but i'm afraid that this will take long
time of computing, and I just reading and learning about TI or other
methods for free energy calculation, so this will be a long time project
However, while I try to put the MD to work for this methods, i need to
know if there is another, maybe not very accurated, energy parameter,
derived from GROMACS MD to take into account before the TI attemp.
Free energy of binding of two proteins in explicit solvent will indeed
be an expensive computation. The obvious cheap alternative is the free
energy of binding in implicit solvent, which will be orders of magnitude
cheaper. You can't use GROMACS though... try APBS.
Mark
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