Re: [AMBER] simulation of protein

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Fri, 4 Jun 2010 10:22:59 -0700

> In context of my previous mail the helix is getting unfolded and sometimes
> sheets are disappearing as well because of 2.1ns md simulation in water at
> constant pressure.Which structure shall I take and the reason for unfolding.

It would help to send your production mdin.
Also your equilibration mdin's to see how well-equilibrated things are.
Did you graph the energy and density to be sure they were equilibrated?

Your homology model might be wrong, but it could also be your
equilibration. One thing that would be interesting to try would
be to switch to constant volume once density is correct.


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Received on Fri Jun 04 2010 - 10:30:07 PDT
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