Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10?

From: Bill Ross <>
Date: Tue, 13 Apr 2010 09:57:28 -0700 (PDT)

This mdin seems like a fast-warming regime that I would hesitate to
even call equilibration:

  irest = 0,
  tempi = 300.0,
  temp0 = 300.0,

Have you looked at your structure to see if it's reasonable?
Normally one equilibrates by slow warming and/or keeping the
solute fixed with restraints.

It will be interesting to see how replicable your results are
in the parallel execution situation.


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Received on Tue Apr 13 2010 - 10:00:05 PDT
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