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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