From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Mon Jun 25 2007 - 07:05:35 CDT
Jerome, thank you for the tip. ABF now works without the energy
minimization.
On 6/24/07, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
>
> Hi again,
> ABF will not work when doing energy minimization. You have to make it
> a separate config file and a separate simulation.
> Best,
> Jerome
>
> On 6/24/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
> > Hi,
> >
> > I am trying to use ABF to constrain dihedral angles. However, the script
> > crashes giving me an error "can't read forces(80)" etc (please see
> output
> > below). Can someone suggest something ? The ABF part of the config file
> and
> > the error output are below.
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> > INPUT:
> >
> > ######################################
> > abf restraintList {
> > d1 {dihe {PRO1 1 C} {PRO1 2 N} {PRO1 2 CA} {PRO1 2 C} 40.0 -60}
> > d2 {dihe {PRO1 2 N} {PRO1 2 CA} {PRO1 2 C} {PRO1 3 N} 40.0 -45}
> > }
> >
> > abf coordinate distance
> > abf abf1 5
> > abf abf2 80
> > abf dxi 0.2
> > abf xiMin 4.0
> > abf xiMax 15.0
> > abf outFile abf_AA.pmf
> > abf inFiles {}
> > abf historyFile abf_AA.hist
> > abf fullSamples 200
> > abf forceconst 0.0
> > #abf applybias no
> > #}
> > ######################################
> >
> > OUTPUT:
> >
> > ######################################
> > CL: ABF> ---------------------------------------------
> > TCL: ABF> Adaptive Biasing Force protocol version 1.6
> > TCL: ABF> ---------------------------------------------
> > TCL: ABF>
> > TCL: ABF> Using coordinate type : distance
> > TCL: ABF> Distance between two atoms (beware of constraints!)
> > TCL: ABF> dxi : 0.2
> > TCL: ABF> dSmooth : 0.3 [default]
> > TCL: ABF> temp : 313
> > TCL: ABF> outFile : abf_AA.pmf
> > TCL: ABF> fullSamples : 200
> > TCL: ABF> writeFxiFreq : 0 [default]
> > TCL: ABF> writeXiFreq : 0 [default]
> > TCL: ABF> abf2 : 80
> > TCL: ABF> fMax : 60.0 [default]
> > TCL: ABF> outputFreq : 5000 [default]
> > TCL: ABF> inFiles : [default]
> > TCL: ABF> historyFile : abf_AA.hist
> > TCL: ABF> df : 1.0 [default]
> > TCL: ABF> moveBoundary : 0 [default]
> > TCL: ABF> distFile : none [default]
> > TCL: ABF> forceConst : 0.0
> > TCL: ABF> xiMin : 4.0
> > TCL: ABF> xiMax : 15.0
> > TCL: ABF> abf1 : 5
> > TCL: ABF> Accumulating force data in 55 bins
> > TCL: ABF> Restraint d1 is a dihedral angle
> > TCL: ABF> Atoms: (13 15 17 23) k : 40.0 kcal/mol/rad Ref: -60.0deg
> > TCL: ABF> Restraint d2 is a dihedral angle
> > TCL: ABF> Atoms: (15 17 23 25) k : 40.0 kcal/mol/rad Ref: -45.0deg
> > Info: Entering startup phase 8 with 7244 kB of memory in use.
> > Info: Finished startup with 7244 kB of memory in use.
> > TCL: Minimizing for 0 steps
> > TCL: ABF> Data written to output files at timestep 0
> > ETITLE: TS
> BOND ANGLE DIHED IMPRP
> > ELECT VDW BOUNDARY MISC
> > KINETIC TOTAL TEMP TOTAL2 TOTAL3
> > TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG
> > GPRESSAVG
> >
> > ENERGY: 0 759.2467 3014.4852 18.1991
> 0.0170
> > -4611.3194 99999999.9999 0.0000 0.0000
> > 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999
> > 0.0000 99999999.9999 99999999.9999 20772.8250
> 99999999.9999
> > 99999999.9999
> >
> > OPENING EXTENDED SYSTEM TRAJECTORY FILE
> > TCL: Minimizing for 10000 steps
> > TCL: can't read "forces(80)": no such variable
> > FATAL ERROR: can't read "forces(80)": no such variable
> > while executing
> > "vecsub $forces($abf2) $forces($abf1)"
> > (in namespace eval "::ABF::ABFcoord" script line 8)
> > invoked from within
> > "namespace eval ABFcoord {
> >
> > set dr [vecsub $coords($abf2) $coords($abf1)]
> > set nv [vecnorm $dr] ;# unity vector
> >
> > loadtotalforces forces
> >
> > set df [ve..."
> > (procedure "ABForce" line 3)
> > invoked from within
> > "ABForce"
> > (in namespace eval "::ABF" script line 30)
> > invoked from within
> > "namespace eval ::ABF {
> >
> > # First timestep : we don't have forces
> > if { $timestep == 0 } {
> >
> > # must not be equal to $timestep - 1
> > set timeStored -2
> > ..."
> > (procedure "calcforces" line 2)
> > invoked from within
> > "calcforces"
> > ######################################
> >
> >
>
-- Maria G. Technical University of Denmark Copenhagen
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