From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jun 26 2007 - 09:44:13 CDT
Hi Adam,
rather than modifying one of the charmm topology files, you're probably
better off just making a new one for hexadecane. There's a tutorial for
this procedure posted at
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/,
which should help you get started. The big trick is going to be figuring
out what parameters to use for your atoms; you've got a choice between
co-opting some from the CHARMM forcefield, making your own from QM
calculations, or finding a good hydrocarbon forcefield from some other
source and translating it into a form that NAMD understands. The
"parameterizing a novel residue" tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/)
helps to give an idea of the issues involved, although in your case I'm
almost certain that you should be able to find good parameters somewhere
in the literature (or, failing that, use appropriate C/H types from CHARMM).
Peter
Adam Fraser wrote:
> Hello, my name is Adam,
>
> I'm doing some research with hydrocarbons that requires MD simulation.
> The molecule of interest is Hexadecane (C16H34). So far my
> experience is limited. I've only done a handful of experiments with
> small polypeptide chains. So I've been looking around quite a bit for
> tutorials and documentation on how to go about preparing and
> conducting this sort of simulation, but have been coming up pretty
> dry.
>
> So far I have created a pdb file of Hexadecane that I've been able to
> successfully view in VMD and calculate Hydrogen positions using one of
> its modelling tools.
>
> What I'm trying to do now is generate a psf file. It looks like the
> best way to do this might be to create my own topology file for atoms
> in Hexadecane.... still I'm sure there's an easier way, and I was
> wondering if anyone has any suggestions?
>
> For example, is it possible to modify my pdb file so I can use the
> top_all22 topology file to generate my psf?
>
> Any input would be greatly appreciated!
>
> Thanks very much.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:53 CST