AMBER Archive (2006)

Subject: AMBER: how to combine NEB method with QM/MM approach

From: caoch_at_cherry.bio.titech.ac.jp
Date: Mon Oct 09 2006 - 11:23:07 CDT

hello all:

  i want to study a proton transfer recation pathway using QM/MM-MD
approach with NEB method.
  
  My questions are
 I) Can such calculation be done only by PIMD?
  if it is not, should such calculation be divided into two steps? (i.e.
extract structures by NEB method and compute energy by QM/MM method)

 II)it seems NEB is used for studying conformation changes in AMBER. in
the case of studing recation, how can I get good structures along recation
pathway by NEB methods?Is it necessary to give enough initial structures
before starting NEB calculation?
 
 III) Are there some references for such study done by amber9?

 any advice is welcome
 
 best regards

                                                        caoch 

-- 
caoch_at_cherry.bio.titech.ac.jp
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