Re: getting desired angle

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 24 2010 - 18:06:00 CDT

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?

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.

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