Re: [AMBER] water molecules

From: M. L. Dodson <>
Date: Wed, 22 Dec 2010 08:04:20 -0600

On 12/22/2010 6:48 AM, Beale, John wrote:
> I am performing MD simulations of the unfolding of a protein in explicit water. I would like to know how to determine and plot the number of water molecules entering the unfolding protein structure over the trajectory. Can someone point me in the right direction to do this?
> John

I'm not sure this is exactly what you want, but how about measuring
hydrogen bonds to backbone atoms as a proxy for unfolding?

Bud Dodson
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
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Received on Wed Dec 22 2010 - 06:30:04 PST
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