From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Thu Mar 06 2014 - 07:23:29 CST
Hello Roy,
My interpretation of Kenno's link to a wiki with the most fundamental
concepts of thermodynamics is his way of saying that
p V = n R T
with n being the number of molecules and V being volume. It's an ideal
gas state equation. Notice that n/V is your density.
In your molecular dynamics, n does not change, so, if you want to keep
the density constant, you need to run your simulation at constant
volume.
Do I get it right Kenno?
In the "NAMD TUTORIAL" pdf, section 1.7.1, find the part that talks
about the NVT esemble. The tutorial is a companion to a group of files
from a molecular dynamics course or workshop. You should be able to
find the example configuration file there.
I hope I am being useful.
Ivan
Ivan Gregoretti, PhD
Bioinformatics
On Wed, Mar 5, 2014 at 5:51 PM, Kenno Vanommeslaeghe
<kvanomme_at_rx.umaryland.edu> wrote:
> On 03/05/2014 04:43 PM, Roy Fernando wrote:
>>
>> I appreciate any advise/suggestion.
>
>
> My advice is to pick up a basic thermodynamics textbook.
> http://en.wikipedia.org/wiki/Equation_of_state#Major_equations_of_state
>
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