RE: modifying cut off

From: Michel Espinoza-Fonseca (
Date: Thu Apr 07 2005 - 19:01:03 CDT




From: Michael Grabe []
Sent: Thursday, April 07, 2005 7:01 PM
To:; Michel Espinoza-Fonseca
Subject: Re: namd-l: modifying cut off


Are you using PME for your calculations?




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!







Michael Grabe, Ph.D.


Genetics Development & Behavioral Science Building

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