Re: Free Energy Calculation of a protein

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Dec 16 2009 - 08:41:50 CST

Thank you all for your responses. The issue is much clearer to me now.
Best,
Mert

On Tue, Dec 15, 2009 at 11:40 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 2009/12/15 Mert Gür <gurmert_at_gmail.com>:
> > I believe due to our point of view ,our understanding of work potential
> is
> > different. I still believe that water can be treated as an T,P reservoir
> > since waters temperature and pressure is constant.
>
> mert,
>
> i think you are mistaken here. even if you use an NTP integration
> algorithm,
> temperature and pressure are by far not constant. they fluctuate a lot.
> they
> become constant only if you have an infinitely large system. for any finite
> system, and particularly the (small) systems that you can treat in a
> typical
> MD simulation, you need a quite long trajectory to average over in order
> to approach a constant temperature or pressure requirement.
>
> cheers,
> axel.
>
> > Best,
> > Mert
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>

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