From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Apr 08 2005 - 09:59:37 CDT
Look for papers by Daggett et al. on cutoffs.
There was a recent publication in December in Biochemistry address the
issue of cutoffs and helical peptides were the models they used...
http://dx.doi.org/10.1021/bi0486381
Regards
Brian
On Thu, 7 Apr 2005, Michael Grabe wrote:
> Are you using PME for your calculations?
>
> -michael
>
> On Apr 7, 2005, at 4:30 PM, Michel Espinoza-Fonseca wrote:
>
> > Hi all,
> >
> > I have a technical question. I?m running MD simulations of peptides to
> > see the effect of phosphorylation. Originally I used a cutoff of 12 A,
> > and now I changed it to 9 A. Interestingly, I obtained different
> > results; for example, the unphosphorylated peptide remained more or
> > less stable as a helix using the 12 A cutoff, while changing it to 9
> > starts to unfold at around 5 ns. So I?m wondering if anybody knows an
> > article where the cutoff has been systematically modified, and how
> > this cutoff (particularly using NAMD) affect the results of the
> > simulation. I?m really interested in that because certainly the effect
> > of phosphorylation on the stability would be led by the electrostatic
> > term in the system.
> >
> > Thank you very much!
> >
> > Cheers,
> >
> > Michel
> >
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> HHMI/UCSF
> Genetics Development & Behavioral Science Building
> 1550 4th Street, GD 481
> San Francisco, CA 94143-0725
> tel: ++ 415.476.0421
> http://itsa.ucsf.edu/~mgrabe
>
>
>
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
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