[AMBER] An issue with conformational changes during MD.

From: Abhilash J <md.scfbio.gmail.com>
Date: Mon, 17 Oct 2016 18:54:21 +0530


  I have a protein with high degree of conformational change. If i prepare
a box which will accommodate both confomations (starting and ending) using
AMBER the resultant box is so big that it will slow the simulations from
current 8 ns/day to 1.5ns/day. The big box in which case is then simulating
primarily water molecules.
  Can i use a smaller box (rather more fitting) in starting then keep
changing the box as the conformation changes. In this case i will need to
somehow save the velocities of protein atoms and immerse it in new water
box. I understand in this case velocities of water atoms is lost. I have
never heard of such simulation and doubt if it is possible.
  Is there a workaround which i can use.
  Please advice.


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Received on Mon Oct 17 2016 - 06:30:02 PDT
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