Re: Calculating macroscopic properties

From: poker_at_physics.usyd.edu.au
Date: Wed May 02 2007 - 22:00:28 CDT

Thanks everyone, I only have crystal structures of the solid and their
IR/Raman spectrums at the moment, and not the more physical properties
like diffusion constant. There are MP staudies lying around, though.

On Tue May 01 2007, Marcos Sotomayor wrote:

>Hi,
>
>Yes, you can perform molecular dynamics simulations with NAMD and get
>macroscopic properties of your system (if its big enough and you sample
>enough as pointed out by Mark). For instance, the pair distribution
>function is usually used to test water models. You can also compute
>diffusion constants, melting temperature (which is likely unreliable
>because the CHARMM force-field is not really designed to account for
>temperature dependence of molecular properties), electrostatic
>potentials, order parameters, etc. Check out the NAMD tutorial (chapter
>2)
>http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
>and the book "Computer Simulations of Liquids" by Allen&Tildesley.
>
>Marcos
>
>On Tue, 1 May 2007, poker_at_physics.usyd.edu.au wrote:
>
>> I have parametrised a pyroglutamic acid residue using CHARMm27 topology
/
>> parameters, and I wanted to test what I have against experimental
>> properties. Is there a way to calculate things like melting point in
NAMD,
>> or do I need to use something else?
>>
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