Query regarding ABF Tutorial on Methane Hydration

From: Navendu bhatnagar (navendu.bhatnagar_at_gmail.com)
Date: Tue Jun 22 2010 - 14:52:41 CDT


This is reagrding ABF-Tutorial on 'Calculation of hydration free energy of
I am trying to reproduce the PMF plot in the analysis section but have not
been able to do so.
Relevant files used in this work have been attached.
Steps as mentioned in the tutorial were followed and here is a brief
description of my implementation:

1. Generated a .psf file from the provided .pdb and topology files.
2. Solvated the system (15 A on all sides)
3. PBC set to 30. 30. 60. to generate vacuum in the z-direction.
4. Minimized and heated the system to 300 K. Equilibrated for 1.0 ns
5. Performed ABF calculations using the parameters as provided in the
abf.conf file (reaction coordinate was split into 5 windows)
6. Created the plot by extracting data from .pmf file

Following is the list of issues/queries :
1. Free Energy profile averages around zero rather than dipping to -3.0
2. Visualization of the simulation trajectory in VMD shows,
    - water box flattens in the x-y direction (probably because 'wrapwater'
command is turned off). Is this correct ? (Please refer to the attached
.dcd file)
    - Methane molecule does not follow a standard path in the z-direction (I
thought that it would follow a 1-D path in the z-direction moving out from
the water phase into the gas phase. Please correct me if I am wrong)
3. How important is it to break the simulation into separate windows ? I
have performed the simulation using both methods ( full vs broken reaction
Simulations were also performed with 'wrapwater' command set to 'on', but
the resulting free energy profile was still incorrect compared to the
Tutorial analysis.
Kindly suggest if there is a basic flaw in my system set up or simulation
that is resulting in this error ? Does this have something to do with
Standard state correction ?

Thanks for your time and help.


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