[AMBER] free energy calculation of folding

From: Asmita Gupta <asmita4des.gmail.com>
Date: Thu, 28 Jan 2016 17:44:33 +0530

Dear users,

  I performed an SMD simulation on a simple RNA duplex structure and
calculated the associated PMF values using Jarzynski equality. From SMD
trajectory, i have extracted structures at different stages of distortion.
  I removed the external restraints from these structures and performed
relaxed conventional MD on them to see how many native contacts can be
regained from each stage. Can you please suggest how i can monitor the
free energy profiles of these relaxed simulations ?


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Received on Thu Jan 28 2016 - 04:30:03 PST
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