RE: Calculating macroscopic properties

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 01 2007 - 01:13:35 CDT

It's unlikely you could reproduce or even recognize liquid/solid transitions
in a simulation with any accuracy. In fact, you probably wouldn't even care
to, unless that was very important to your simulation.

More commonly used are things such as high resolution crystal structures,
vibrational spectra, etc. Also important are comparisons between simulation
and QM calculations; in fact, Charmm is parameterized such that interaction
distances and energies of every atom with TIP3P water agrees with QM
calculations.

You may also find the VMD plugin Paratool helpful for calculating the full
set of parameters such as bonds, angles, dihedrals, etc.

In any case, I'm a little surprised it hasn't been done before...
 

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of poker_at_physics.usyd.edu.au
Sent: Monday, April 30, 2007 9:39 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Calculating macroscopic properties

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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