From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Jan 05 2010 - 11:44:58 CST
Dear Austin:
1) xiMin and xiMax are boundaries of the grid used to collect data,
but the system is free to evolve between them.
2) you are using an older version of the code. The current version is
part of the "collective variable calculations" module of NAMD 2.7 and later.
3) any data analysis software should be able to read the files (the
are plain text). I like xmgrace and gnuplot.
Best,
Jerome
2010/1/5 Austin B. Yongye <ybausty_at_yahoo.com>:
> 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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