[gmx-users] Fast energy parameter

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jul 4 00:56:24 CEST 2009

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.


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