Re: modifying cut off

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Thu Apr 07 2005 - 19:00:31 CDT

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. Iím 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 Iím 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. Iím 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
>
------------------------------------------------------------------------
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Michael Grabe, Ph.D.
HHMI/UCSF
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tel: ++ 415.476.0421
http://itsa.ucsf.edu/~mgrabe

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