Re: How to maintain Density constant?

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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