From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Mon Jul 30 2007 - 08:58:58 CDT
Hi Arun,
The error means that ${inprot}.xsc can't be opened. Make sure that this file
exists in the directory.
Justin
On 7/30/07, Arun Krishnan <krishnan_at_ttck.keio.ac.jp> wrote:
>
> Hi Folks,
>
> I am trying to do an MD simulation for a simple test example using
> ubiquitin. I first do an energy minimization, followed by heating to 300K.
> After this, when I try to do an equilibration run, I get the error:
>
> FATAL ERROR: Unable to open extended system file.
>
> My equilibration config file looks like this:
>
> ######################TOSET############################
> # molecular system
> set MOL 1UBQ_PandS_wb
> structure ${MOL}.psf
>
> # after heating.
> set inprot ${MOL}_heat
> coordinates ${inprot}.coor
> velocities ${inprot}.vel
> extendedSystem ${inprot}.xsc
>
> set temperature 300 ;# the temperature
>
> set outputname ${MOL}_eq
> set eq_restart ${MOL}_eq_restart
>
> firsttimestep 0 ;# reset to 0 for equilibration run.
>
> fixedAtoms off
>
> # force field
> paratypecharmm on
> parameters ../topology_files/toppar/par_all22_prot.inp
> exclude scaled1-4
> 1-4scaling 1.0
>
> cellBasisVector1 72.165 0.0 0.0
> cellBasisVector2 0.0 74.867 0.0
> cellBasisVector3 0.0 0.0 77.663
> cellOrigin 30.5597000122 30.3731307983 17.1436786652
> wrapAll on
>
> PME on
> PMEGridSizeX 75 # size along cellBasisVector1.
> PMEGridSizeY 75 # along cellBasisVector2.
> PMEGridSizeZ 80
> # use numbers with small integer factors: 2,3,5.
>
> # approximations
> switching on
> switchdist 10
> cutoff 12
> pairlistdist 13.5
>
> # center-of-mass motion is automatically removed.
>
> # integrator
> timestep 1.0 ;# in fs.
> stepspercycle 20 ;# default
> nonbondedFreq 2 ;# same as BerendsenPressureFreq
>
> fullElectFrequency 2
>
> # output
> outputName $outputname
> dcdfreq 1000 ;# every ps
> xstFreq 1000
> outputEnergies 1000
> outputPressure 1000
> outputtiming 1000
> binaryoutput no
>
> # for restarting:
> restartname $eq_restart
> restartfreq 10000
> restartsave yes
> binaryrestart no ;# yes will preserves more accuracy.
>
> # Temperature coupling via Langevin dynamics.
> langevin on
> langevinTemp $temperature
> langevinDamping 1.0 ;# from mailing-list
>
> langevinHydrogen on
>
> # Pressure coupling by Nose-Hoover Langevin piston pressure control
> LangevinPiston on
> LangevinPistonTarget 1.01325 ;# in bar.
> LangevinPistonPeriod 200 ;# in fs.
> LangevinPistonDecay 100
> LangevinPistonTemp $temperature ;# set same as langevinTemp.
>
> # GPressure seems to fluctuate about 1.0, betw -2K to 2K.
>
> useGroupPressure yes # use hydrogen-group based virial. use with
> rigidBonds.
>
> # GROMACS: ref_p = 1.0 bar; compressibility = 4.5e-5 bar-1; tau_p = 0.5 ps
> # but tau_p = 0.1ps gave errors.
>
> margin 3.0 ; # increase margin to overcome problem with
> decreasing cell size.
>
> # to use SHAKE to constraint all bonds during free MD only.
> rigidBonds all
>
> # short equilibration run
> run 50000 ; # 50 ps
>
> Has anyone come across this error before. Or can anyone spot some obvious
> problem with my configuration file?
>
> Thanks,
>
> Arun
>
>
> --
> ***********************************************
> Arun Krishnan, Ph.D,
> Assistant Professor,
> Institute for Advanced Biosciences,
> Keio University,
> Center Building,
> Tsuruoka, Yamagata 997-0035
> Japan
> Phone: +81 (0)235-29-0824
> Email: krishnan_at_ttck.keio.ac.jp
> URL: http://www.iab.keio.ac.jp/~krishnan
> **********************************************
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