ABF questions

From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Tue Jan 05 2010 - 10:27:47 CST

Dear all,
I am trying to apply ABF during a simulation. I have read the ABF section in the NAMD27b1_Documentation file and the ABF-Mar2008 tutorial. Please I have some questions:

1). Is the distance between abf1 and abf2 decreased/increased progressively from xiMax to xiMin in the course of the simulation; or are xiMax and xiMin simply used as limits for creating bins, and then energies are computed for structures in each bin?

2). What keyword should I use to generate the .grad, .count and .pmf output files? My current output does not include these files.

3). What tools do I need to generate the free energy plot for the simulation (e.g. Figure 1 of the ABF-Mar2008.pdf tutorial)?

Thanks,
Austin-

My configuration and abf.tcl files are included below:

#protocol params
numsteps 20000

#initial config
ambercoor ../3mem3mem.crd
parmfile ../3mem3mem.top

#output params
outputname 3mem3mem_min
binaryoutput on

#force field params
paraTypeCharmm off
amber yes
parameters parm94.dat
exclude scaled1-4
scnb 2.0
1-4scaling 0.83
switching off
switchdist 8.0
cutoff 12.0
pairlistdist 14.0
pairlistsPerCycle 2
margin 0.0
stepspercycle 20
rigidBonds all
timestep 0.5

#dcd file
DCDfile 3mem3mem_atombased.dcd
DCDfreq 10

temperature 300

#abf section
source ./Tutorial-ABF/abf-1.8/abf.tcl
abf coordinate distance
abf abf1 90
abf abf2 59
abf xiMin 1.45
abf xiMax 9.00
abf dxi 0.1
------------------------------------------------------

         #############################################
         # Generic ABF code #
         # Jerome Henin <jerome.henin_at_uhp-nancy.fr> #
         #############################################

############
# Startup #
############

package provide abf 1.7.0

#########################
# Parameter definitions #
#########################

namespace eval ::ABF {

set version "1.7"

if {! [info exists ABFdir]} { set ABFdir [file dirname [info script]] }
# If it fails, try the local directory
if { $ABFdir == "" } { set ABFdir "." }

TclForces on
TclForcesScript $ABFdir/abf_script.tcl

array set defaults {
inFiles {}
outFile atom_based_01.dat
outputName 3mem3mem_abf
historyFile none
distFile distfile_abf.dat
forceConst 500.0
fullSamples 500
outputFreq 100
df 1.0
fMax 60.0
dSmooth 0.0
writeXiFreq 100
writeFxiFreq 100
usMode no
applyBias yes
moveBoundary 0
temp 300.0
abf2 {}
}

set mandatory "coordinate xiMin xiMax dxi abf1"

# these settings are not displayed at startup
set silent "restraintList usMode SFM applyBias direction abf3"

array set capitals {}
foreach param [concat $silent $mandatory [array names defaults]] {
    set capitals([string tolower $param]) $param
    # not set yet
    set alreadySet($param) 0
}

} ;# namespace

proc abf { keyword value } {
    set ::ABF::keyword $keyword
    set ::ABF::value $value

namespace eval ::ABF {

    # Build list of all allowed parameter names
    set list [array names capitals]

    set lowercase [string tolower $keyword]

    # Process parameters
    if {[lsearch $list $lowercase] != -1} {
        set keyword $capitals($lowercase)

        if { $alreadySet($keyword) } {
            print "ABF> WARNING - multiple definitions of parameter " $keyword
        }

        set $keyword $value
        set alreadySet($keyword) 1

        return
    } else {
        error [format "Unknown ABF keyword: %s" $keyword]
    }

} ;# namespace
} ;# proc abf

# define upper-case synonyms to proc abf
proc ABF { keyword value } {
    abf $keyword $value
}
proc Abf { keyword value } {
    abf $keyword $value
}

      

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