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