Dear List,
There are number of techniques implemented in AMBER such as REMD, H-REMD,
aMD, SMD and gaMD. In my view aMD methods and its enhancements (SMD, gaMD)
are computationally less expensive since these techniques only require one
simulation as compared to multiple replicas in REMD.
I saw paper by Daniel Roe on a very long simulation of nucleotide using
combination of techniques such as aMD and H-REMD. In my view running long
simulation using enhanced sampling techniques (for protein folding) doesn't
guarantee convergence. I was interested in knowing how can we assure
whether a simulation has converged or not or whether a particular enhanced
technique will do a better job over the other? Are running multiple
simulations is one of the measure to look at statistically significant
convergence?
Any insight on the above matter is appreciated.
Regards,
Neha
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Received on Wed Jun 22 2016 - 06:00:06 PDT
