[gmx-users] total simulation time for proteins in general

Erik Lindahl lindahl at cbr.su.se
Wed Apr 11 08:36:39 CEST 2007


On Apr 11, 2007, at 7:26 AM, Priya Chandran wrote:
> 2. Is minimisation in GROMACS only used as a precursor to the md- 
> simulation to remove bad contacts, or can we also use it  
> effectively to minimize a raw modelled ab-initio structure.?

Well, technically you can of course use it, but any energy  
minimization algorithm will only take you to a close local minimum in  
the energy (=enthalpy) landscape.

If you want your model to get closer to the native state you need  
refinement, and that's way more complicated. Search the literature  
for techniques like simulated annealing, Replica-exchange molecular  
dynamics, etc.



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