Unfolding protocol..

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Fri Aug 03 2007 - 00:58:58 CDT

Dear All,

I am trying to unfold a small protein and here is what I think the protocol
is. I would appreciate it if someone knowledgeable about unfolding
simulations could let me know if this is ok or not:


   Input: Protein in water box (periodic boundary conditions)
   (a) Energy minimization of protein + water box - 3000 ps - 1fs timestep
   (b) heat to 300K - 7000ps - 1fs timestep
   (c) equilibrate @ 300K - 1ns - 2fs timestep
   (d) Heat to 500K - 7000ps - 1fs timestep
   (e) equilibrate @ 500K - 1ns - 2fs timestep


   production run for 8ns - 2fs time step


(1) Should I do an energy minimization before the production run in NVT?
(2) Should the equilibration at 500K be done under NVT conditions?

Any help will be much appreciated.



Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Phone: +81 (0)235-29-0824
Email: krishnan_at_ttck.keio.ac.jp
URL: http://www.iab.keio.ac.jp/~krishnan

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:02 CST