From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun Jun 24 2007 - 11:41:04 CDT
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: -60.0 deg
> TCL: ABF> Restraint d2 is a dihedral angle
> TCL: ABF> Atoms: (15 17 23 25) k : 40.0 kcal/mol/rad Ref: -45.0 deg
> 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"
> ######################################
>
>
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