Re: Problems with minimization

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Sat Nov 15 2008 - 11:38:26 CST

Diego,

You say collapsed, what exactly do you mean by collapsed? What does
the xsc file look like? Since this is just minimization there should
be one line. Also for the log file what is the command line syntax
you used to run NAMD? If you didn't redirect the output to a file it
displays in your Std out.

Chris

On Nov 15, 2008, at 11:57 AM, Diego Alejandro Vargas wrote:

> Hi everybody,
> I am running 10000 minimization steps for the Beta chain of fascin
> in a water box. The simulation appears to run properly and
> terminates successfully. But when I look at the dcd file, the water
> box is collapsed from the first frame. I generated the psf file
> through the automatic psf generator in VMD and solvated it using the
> solvate package (I followed the tutorial for ubiquitin). Also, I
> don't get a log file as an output; I don't understand why.
>
> Does anybody know why this is occurring? The configuration file is
> copied below. Let me know if you have any questions.
>
> Thank you,
> Diego A. Vargas
> _________________________________________________________
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ***
> coordinates ***
>
> set temperature 310
> set outputname ***
>
> 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
> 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
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 48. 0. 0.
> cellBasisVector2 0. 58. 0.
> cellBasisVector3 0. 0 46.
> cellOrigin 62. 89. 10.
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 50
> PMEGridSizeY 50
> PMEGridSizeZ 50
>
>
> # 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.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 10000
>

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