From: nabaneeta mukhopadhyay (nabaneeta85_at_gmail.com)
Date: Thu Sep 20 2012 - 11:21:33 CDT
My system consists two single wall carbon nanotubes in aqueous dispersion.
Each tube consists 260 atoms. I want to calculate PMF of the system using
Umbrella Sampling technique by *varying separations * (7-18 angstrom) along
x-axis between the two tubes. I am applying a harmonic potential of force
constant = 0.5
I start at a separation of 18 angstrom between the tubes and then
eventually decrease the separation along x-axis (17, 16 , 15,........,7
angstrom). Simulation time at each step is is 1 ns.
I am going to use colvar for umbrella sampling purpose. For that I have
prepared the input file given below. I am a newbie in this field and I'll
really appreciate if someone can let me know whether this is a correct
method or not.
# colvar config file
#output values every 100 steps
targetCenters 18.0 17.0 16.0 15.0 14.0 13.0 12.0 11.0 10.0 9.0 8.0
force constant 0.5
Thank you in advance, for your time and consideration in answering my query.
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