From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Mar 15 2012 - 09:19:20 CDT
Those errors seem quite self-explanatory, you haven't included cutoff,
exclude, or outputname in your config file. I know I can see them in your
message, but maybe get rid of the if statement and just make a plain config
file to start until you get it working.
Also, any particular reason to use NAMD 2.7b2 rather than 2.8?
~ARon
On Thu, Mar 15, 2012 at 8:20 AM, upayan baul <margheritan22_at_gmail.com>wrote:
> Hi,
> I am very new to using NAMD. I am trying to equilibrate a box of water in
> steps. The first run works but I'm unable to restart it. Please point out
> my mistake. I attach the error message in log file too.
>
> The input files exist in the directory.
>
> Rehards,
> Upayan
>
>
> structure ../water/solvate.psf
> coordinates ../water/solvate.pdb
>
> set temperature 298
> set outputname wb_eq2
>
> # Continuing a job from the restart files
> if {1} {
> set inputname wb_eq1
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel
> extendedSystem $inputname.restart.xsc
>
> temperature $temperature
> minimize 100
> reinitvels $temperature
>
> }
>
> firsttimestep 200001
>
>
> # Input
> paraTypeCharmm on
> parameters ../water/par_all27_prot_lipid.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude 1-3
> #1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 1fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 48.0 0. 0.0
> cellBasisVector2 0.0 25.0 0.0
> cellBasisVector3 0.0 0 48.0
> cellOrigin 23.90 12.51 23.99
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> #PMEGridSpacing 1.0
>
> #manual grid definition
> PMEGridSizeX 60
> PMEGridSizeY 60
> PMEGridSizeZ 60
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.0
> langevinPistonDecay 50.0
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
>
> # Minimization
> minimize 100
> reinitvels $temperature
>
> run 200000 ;
>
>
> log file:
> Charm++: standalone mode (not using charmrun)
> Charm++> cpu topology info is being gathered.
> Charm++> Running on 1 unique compute nodes (2-way SMP).
> Info: NAMD 2.7b2 for Linux-x86
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60103 for net-linux-iccstatic
> Info: Built Thu Nov 12 22:11:41 CST 2009 by jim on kyoto.ks.uiuc.edu
> Info: 1 NAMD 2.7b2 Linux-x86 1 as38 upayanb
> Info: Running on 1 processors.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 27360.5 s
> Info: 1.22376 MB of memory in use based on CmiMemoryUsage
> Info: Configuration file is wb_eq.conf
> TCL: Suspending until startup complete.
> ERROR: 'cutoff' is a required configuration option
> ERROR: cutoff defines: local electrostatic and Vdw distance
> ERROR: 'exclude' is a required configuration option
> ERROR: exclude defines: Electrostatic exclusion policy
> ERROR: 'outputname' is a required configuration option
> ERROR: outputname defines: prefix for the final PDB position and
> velocity filenames
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> [0] Stack Traceback:
> [0] _ZN9NamdState14configListInitEP10ConfigList+0x369 [0x84aadcd]
> [1] _ZN9ScriptTcl9initcheckEv+0x54 [0x84fd338]
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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