Re: Free Energy Calculation of a protein

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 15 2009 - 03:40:07 CST

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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