From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Wed Feb 05 2020 - 12:12:29 CST
Hello,
My objective is to apply flat-bottom harmonic position restraints to the
C-alpha (CA) atoms. To achieve this, I am using the colvars harmonicWalls.
I have a question regarding setting the values of lower and upperWalls,
with respect to the reference CA positions.
Typically, a regular harmonic position restraint is applied, where a
reference PDB is provided as an input to the parameter consref. My
question, is can we pass a reference pdb to colvars and set the upper and
lower bounds with respect to the selection?
Following is my colvar definition. Any help is greatly appreciated.
#########################
colvars on
colvarsTrajFrequency 100
cv config "
colvar {
name calpha
group1 {
psfSegID AP1
atomNameResidueRange CA 1-76
}
}
"
cv config "
harmonicWalls {
name fb_restraint
colvars calpha
lowerWalls * #add_lower_bound_from_ref_CA_position*
upperWalls *#add_upper_bound_from_ref_CA_position*
lowerWallConstant 10.0
upperWallConstant 10.0
}
"
#########################
Thanks,
Daipayan
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