Re: abf output

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Fri Apr 20 2007 - 17:08:47 CDT

Christine,

was does the NAMD output file tell you? Have you looked at the
values of Xi given therein? Do they fall in the [XiMin;XiMax]
range that you have defined?

Chris Chipot

Christine Horejs a écrit :
> Hi everybody!
>
> The .dat file of my abf simulation for a pmf calculation is zero for every xi-step and I can't find the mistake in my configuration file!
> I want to calculate the pmf for a large molecule, when it is unfolded.
>
> Can anybody help me? PLease!
>
> Here is the configuration file and the .dat file:
>
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # Ubiquitin in a Water Sphere
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure sbsb.psf
> coordinates sbsb.pdb
>
> set temperature 300
> set outputname sbsb_pmf
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> # Spherical boundary conditions
> sphericalBC on
> sphericalBCcenter 2.95680737495 38.6497306824 40.4132194519
> sphericalBCr1 107.0
> sphericalBCk1 10
> sphericalBCexp1 2
>
>
> source /hpc_home/rtscheli/NAMD/NAMD_2.6_Linux-amd64/lib/abf/abf.tcl
> package require abf
>
>
> abf coordinate distance
>
>
> abf abf1 5
> abf abf2 13742
>
>
> abf dxi 0.01
> abf xiMin 108.0
> abf xiMax 118.0
> abf outFile sbsb.dat
> abf fullSamples 500
> #abf inFiles {}
> abf distFile sbsb.dist
> abf forceconst 20.0
> abf dSmooth 0.0
> abf applyBias yes
> abf historyFile sbsb.history
> abf writeXiFreq 1000
>
>
>
> ################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 1000
> reinitvels $temperature
>
> run 2500 ;# 5ps
>
> .dat-file:
>
> # xi A(xi) av_force n_samples
> 108.005 0.0000 0.0000 0
> 108.015 0.0000 0.0000 0
> 108.025 0.0000 0.0000 0
> 108.035 0.0000 0.0000 0
> 108.045 0.0000 0.0000 0
> 108.055 0.0000 0.0000 0
> 108.065 0.0000 0.0000 0
> 108.075 0.0000 0.0000 0
> 108.085 0.0000 0.0000 0
> 108.095 0.0000 0.0000 0
> 108.105 0.0000 0.0000 0
> 108.115 0.0000 0.0000 0
> 108.125 0.0000 0.0000 0
> 108.135 0.0000 0.0000 0
> 108.145 0.0000 0.0000 0
> 108.155 0.0000 0.0000 0
>
> I really hope that anybody can help me!
>
> greetings,
> Christine
>

-- 
_______________________________________________________________________
Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1           Phone: (33) 3-83-68-40-97
B.P. 239                                      Fax:   (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex, France
                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr
        Greatness inspires envy, envy engenders spite, spite spawns lies
                                                 Joanne Kathleen Rowling
_______________________________________________________________________

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