Re: getting desired angle

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sun Oct 24 2010 - 22:06:33 CDT

On Mon, Oct 25, 2010 at 7:06 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Oct 23, 2010 at 4:49 AM, Kwee Hong <joyssstan0202_at_gmail.com>
> wrote:
> > Hi.
> > My protein is bound to one cadmium ion.
> > I've inserted the relevant parameter value which I got from the
> literature
> > into the force field file.
>
> did you also define the corresponding interactions, e.g. bonds,
> angles, dihedrals and so on in the .psf file?
>
> They are all auto-defined in the .psf file.

> having parameters in the parameter file alone only works for
> non-bonded interactions.
>
> > After 5ns simulation, I did not get my desired angle at the cadmium ions.
> > Is there anyway I can tackle this?
>
> have you tried running a test system, equivalent to the
> one in the publication that you took the parameters from?
>
> interactions to multi-valent, heavy atoms are difficult to
> model with a simple force field. frequently a significant
> redistribution of charges happens around the ion, which
> would be very much dependent on the specific environment.
>
> cheers,
> axel.
>
> > Thanks
> > Regards,
> > Joyce
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:20 CST