AMBER Archive (2007)

Subject: AMBER: Difference in Equilibration & Production MD in Amber

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Wed Feb 28 2007 - 14:33:56 CST

I am curious if there is some difference in the way an Equilibration Vs
Production molecular dynamics simulation should be setup in AMBER ?

I understand that output options such as NTWX, NTPR etc. should be adjusted
in Production MD. However, my concern is if certain options which affect
simulation should also be altered ???

>From one of the previous posts, I found that TAUP and GAMMA_LN was altered
the following way::

Equilibration Run:
TAUP = 2.0
GAMMA_LN = 1.0

Production Run:
TAUP = 1.0
GAMMA_LN = 5.0

Does this make sense, I will be glad if you have any suggestions on this
issue?

Also, is it a good idea to use IWRAP = 1 or post-processing using ptraj (for
centering images) is better??

Here is one of my equilibration MD file which I used::
------------------------------------------------
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 7,
  ntb = 2,
  ntp = 2,
  pres0 = 1.0,
  taup = 2.0,
  cut = 10,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 25000, dt = 0.002,
  ntpr = 100, ntwx = 2000, ntwr = 1000
------------------------------------------------

I look forward to your suggestions.

Best Regards
Akshay

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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17_at_olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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