Re: A question on minimization

From: Marcos Sotomayor (
Date: Fri Nov 04 2005 - 16:18:46 CST

Did you set up the size of the periodic box and its
center appropriately?


On Fri, 4 Nov 2005, santanu chatterjee wrote:

> Hi,
> I was trying to minimize solvated ww domain ( 39
> residues ). I do not know very well about the
> minimization procedure and what to expect at the end.
> I ran 200 steps of minimization. It looks like the
> protein molecule is
> being pushed at one side. Moreover there is a hole in
> the middle. I am not sure whether this is something I
> should expect after the minimization is complete. Any
> ideas, thoughts, hints will be most welcome since I
> have no idea why it should look like this after
> minimization or is it just some mistake in setting up
> the parameters. I have put the pictures of the
> solvated molecule before and after minimization on the
> web ( The
> second picture clearly depicts the strange behavior.
> Thanks in advance,
> santanu
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