Re: ABF questions

From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Wed Jan 06 2010 - 09:56:28 CST

Hi Branko and Jerome.
I tried your suggestions and the ABF simulation runs smoothly.
Thanks a lot!
Austin-

--- On Wed, 1/6/10, Branko <bdrakuli_at_chem.bg.ac.yu> wrote:

> From: Branko <bdrakuli_at_chem.bg.ac.yu>
> Subject: Re: namd-l: ABF questions
> To: "Austin B. Yongye" <ybausty_at_yahoo.com>, namd-l_at_ks.uiuc.edu
> Date: Wednesday, January 6, 2010, 5:17 AM
>
>
>
>
>
>
>
> Austin,
>
>
>
> You mixed  the ABF definition in 2.6 and 2.7: Just
> transfer ABF section
> from namd configuration (1.emin_colvar.conf) to colvar
> configuration
> (now colVarfile.txt) and uncomment  (delete #) 
> ABF lines, example is
> below:
>
>
>
> abf {
>
>    colvars d
>
>    fullSamples    500
>
>    hideJacobian    no
>
>    outputFreq    1000
>
>    applyBias    yes
>
> }
>
>
>
> Obviously that source - path is unnecessary
>
> Also try to remove extension from colVarfile (without
> .txt), samie in
> NAMD configuration
>
>
>
> colvars section
>
> colvars        on
>
> colvarsConfig    colVarfile
>
>
>
> It should work. When you use one colvar, 27b gives three
> outputs
> <file>.count ,  <file>.grad  ,
> <file>.pmf.
>
> For more details see  2.7b user guide:
> http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/
>
>
>
> Hope this help.
>
>
>
> Branko
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Austin B. Yongye wrote:
>
> 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
> }
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> #collective variables config file
>
> #globalOption value
> colvarsTrajFrequency 100
> colvarRestartFrequency 100
> analysis on
>
> colvar
> {
> name cv1 # needed to identify the variable
>
> # flags to define the behavior of 1st-colvar
> width 0.5
> lowerBoundary 1.0
> upperBoundary 9.0
>
>
> # all the following terms are summed together to provide
> the
> # value of 1st-colvar
> distance
> {
> # configuration for the 1st colvar component
> group1
> {
> atomNumbers {91 92 93}
> }
> group2
> {
> atomNumbers {57 60}
> }
> oneSiteSystemForce yes
> }
>
> }
>
>
>
>
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