Re: [AMBER] Protein moving out of the water box

From: David A Case <>
Date: Sat, 21 May 2016 12:58:05 -0400

On Sat, May 21, 2016, Arati Paudyal wrote:

> I am just surprised how much the
> protein moved during the 80ns simulation. Could you please suggest me some
> appropriate steps from now onward?

I am unable to offer detailed assistance in understanding your results.
But check (for yourself) what you really mean when you say "the protein
moved": did it change conformations? Did it do so in a way that offers
insight into the nature of possible motions in the system? Is it mainly a
change that keeps individual domains more of less intact, but changes the
relative orientation of different domains?

In addition to careful visual inspection of the animations, clustering the
conformations is often a very good way of establishing what sorts of motions
were taking place.


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Received on Sat May 21 2016 - 10:00:03 PDT
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