using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion

From: nabaneeta mukhopadhyay (nabaneeta85_at_gmail.com)
Date: Thu Sep 20 2012 - 11:21:33 CDT

Hello Everyone,

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
colvarsTrajFrequency 100

colvar{
name colvar_dist
OutputSystemForce yes

distance
{
group1
{
atomNumbersRange 1-260
}
group2
{
atomNumbersRange 261-520
}
}
}

harmonic
{
name potential
colvars colvar_dist
centers 18.0
targetCenters 18.0 17.0 16.0 15.0 14.0 13.0 12.0 11.0 10.0 9.0 8.0
targetNumsteps 10000000
targetNumStages 11
force constant 0.5
}

Thank you in advance, for your time and consideration in answering my query.

regards,
Nabaneeta

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