Colvars Configuration File

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sat Aug 15 2009 - 02:16:19 CDT

Dear NAMD community,

I intend to calculate the PMF of a small biomolecule as a function of just
one of its dihedral angles (which I call omega_prime), using the Adaptive
Biasing Force module in NAMD 2.7. This should be s starightforward 1-D
calculation.

For this purpose, I have added the following lines in my namd input file for
an isobaric-isothermal simulation:

###### Collective Variables Section ####################
colvars on
colvarsConfig config_colvars1.inp
colvarsInput config_colvars2.inp

###### ABF Section ####################
fullSamples 100
hideJacobian no
outputFreq 100
# Reading gradient and sampling files:
#inputPrefix
applyBias yes
######################################

*However, I am having a bit of trouble in putting together my colvars input
file. I tried to follow the example and the instructions given in the
manual, to put this together:*
#########################################
globalOption ??
colvar {
        name omgprm
        width 1.0
# Assuming colvars treats dihedrals in degrees:
        lowerBoundary -10.0
        upperBoundary 175.0
# lowerWallConstant 0.03 # Is it necessary to supply these?
# upperWallConstant 0.08
        outputValue on
        outputVelocity off
        outputSystemForce off
        outputAppliedForce on
        extendedLagrangian off
        componentExp 1
        componentCoeff 1.0

# Defining the components:
        colvarOption ??
        dihedral {
                componentOption ??
                componentLongOption {
                        ??
                }
        }

        # atom group definitions:
        myatoms {
                psfSegID TRAN
                atomsFile component.pdb
                atomsCol O
                atomsColValue 4.00
        }
}

biastype1 {
        name ??
        colvars omgprm
}
#########################################

I did not quite understand from the manual what the "globalOption",
"colvarOption", "componentOption" and the "componentLongOption" stand for.
The form of the variable "mybias" is also not clear to me.

Some help with this would be greatly appreciated.

Thanks and regards,
Neelanjana Sengupta

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