From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Apr 07 2005 - 18:30:23 CDT
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!
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