AMBER Archive (2005)

Subject: AMBER: nscm

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Apr 12 2005 - 09:55:50 CDT


Dear all,

I am doing a free energy difference calculation from ethane -> methane in
gas phase. This is a test case. I created the structures in Xleap and did
202 dv/dl simulations for 100 ps.; 101 for nscm=200 and 101 for nscm=50.
Then I used the trapezoidal rule to calculate the integral and here are
the results:

for nscm=50 : Integral = -0.157530606498188
for nscm=200: Integral = -0.199276122465974

Is this something normal to expect when we set the number of steps for
center of mass regulation to different numbers? I would have expected no
change in the results. Did anybody encounter with a similar case? Thanks
in advance.

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------

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