From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Tue May 01 2007 - 11:49:44 CDT
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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