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:

Steps:

NPT
====
   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

NVT
===

   production run for 8ns - 2fs time step

Questions:

(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.

Regards,

Arun

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

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