Re: OPLS force field in namd

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sat Sep 15 2007 - 02:48:56 CDT

OPLS-AA is indeed implimented in NAMD. There are even parameter files
around at this point. I think they are available from the site of
MacKerell.

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

Personally, I build my own, but I am not doing biomolecules. A couple years
ago it was necessary to build your own parameter files, etc., but now most
of the stuff is available. It was also necessary to recompile NAMD to use
the geometric mean for the sigma but as of version 2.6b1 (I think) it is
included as an option

use:

*vdwGeometricSigma yes*
**
*As far as using the SPC/E model, see pages like*
**
http://www.lsbu.ac.uk/water/models.html

for parameters. I personally use vmd to solvate but modify the parameters
(default as TIP3P of course) to be replaced with SPC/E parameters. This is
pretty simple to do (just modify the bond lengths, charges, etc. in the
toplogy, psf, pdb files, etc.)

Other than that, it seems pretty straight forward. If you would like
details about anything, please email me off the list if you want.

Josh

On 9/14/07, Adam Fraser <adam.n.fraser_at_gmail.com> wrote:
>
> Hello all,
>
> I've been poking through the wiki and the old namd-l archives and have
> found little detail on how to run simulations in namd with the OPLS force
> field and SPC/E water model.
>
> I'm running simulations studying the "hydrophobic bond" phenomenon between
> 2 hydrocarbons and would, therefore, like to use the best water model
> possible (without having to resort to anything that will bog down
> computation a lot like I imagine TIP6P would).
>
> Thanks for any help you can give!
> -Adam
>

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