Re: Water molecules inside protein?

From: Stephen Hicks (
Date: Tue Jun 05 2007 - 21:07:47 CDT


I'm not entirely sure I understand what you're asking, but if you're
just looking to track the water molecules, then unwrapping boundaries
for the entire system 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 for just the protein 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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