Re: [AMBER] An issue with conformational changes during MD.

From: Hai Nguyen <>
Date: Sun, 23 Oct 2016 13:22:30 -0400


On Mon, Oct 17, 2016 at 9:24 AM, Abhilash J <> wrote:

> 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.

The only workaround I can think of is to use implicit solvent (e.g GB)
The real benefit is faster sampling and its (GB) speed does not depend on
conformational change.

Otherwise, you might need to use GPU.


> Please advice.
> Regards
> Abhilash
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Received on Sun Oct 23 2016 - 10:30:03 PDT
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