Re: ABF questions

From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Tue Jan 05 2010 - 16:19:57 CST

Dear all: A couple of questions: 1). I used my current version of namd (NAMD_2.7b2) with the initial input files I sent to you, and had this output. See attached file, atom_based_01.dat. Is column2 the file the free energy change at each xi value? Would that then represent the free energy change of the reaction coordinate? 2). I read the collective variables section of the NAMD_2.7b2 manual and prepared the .conf and collective variable files attached. When I run the simulation I get this error message: colvars: Warning: "colvar" keyword found without any configuration. colvars: Error: no collective variables defined. colvars: If this error message is unclear, try recompile with -DCOLVARS_DEBUG. FATAL ERROR: Error in the collective variables module: exiting. I thought of compiling with the -DCOLVARS_DEBUG option, but the colvars subdirectory of my NAMD_2.7b2 has only these two files: colvarproxy_standalone.C and colvarproxy_standalone.h, missing several of the files in the include statement missing. I downloaded the NAMD_2.7b2 source code, but the colvars subdirectory still had only these two files. Any help will be appreciated. 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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