Hi!
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.
Regards
Abhilash
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Received on Mon Oct 17 2016 - 06:30:02 PDT
