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
--
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:10 CST