Re: Water molecules inside protein?

From: Stephen Hicks (
Date: Tue Jun 05 2007 - 11:09:19 CDT


If you're looking to track the water molecules, then unwrapping all
your boundary conditions should be sufficient. You can use your
initial frame as a reference, and then for each successive frame
measure the fit back to the reference frame and apply that
transformation to all molecules, including all the waters. This will
make things look like your protein is more or less stationary.


On 6/5/07, <> wrote:
> Hi All,
> I have been doing an NVE run of my protein with periodic boundary conditions and my protein slowly moves during run, goes out and wrapped to another side of box. ALl that is fine. I want to track the water molecules in the center of protein during all frames. I dont know how to tack them when protein itself is moving and wrapped too. I am not sure doing unwrapping only protein or all system can help anyhow? ANy help from experienced users will do great.
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823

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