Re: ABF questions

From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Tue Jan 05 2010 - 12:10:04 CST

Hi Jerome,
Thanks for the response.
I am using the namd2 executable that came with the NAMD_2.7b2_Linux-x86 distribution. If that's the older version of the code, please how do I point to the new version? If you have an input file that includes the collective variables section, that will be a great start for me.
Thanks,
Austin-

--- On Tue, 1/5/10, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:

> From: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> Subject: Re: namd-l: ABF questions
> To: "Austin B. Yongye" <ybausty_at_yahoo.com>
> Cc: "NAMD" <namd-l_at_ks.uiuc.edu>
> Date: Tuesday, January 5, 2010, 9:44 AM
> 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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