From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 28 2009 - 07:22:34 CST
Vacuum simulations and pressure control don't mix. Your periodic cell is
probably collapsing. Out of curiosity, why are you running in vacuum?
Also, a timestep of 0.000000002 is painfully slow. The namd timestep is
given in fs.
uma mageshwari wrote:
> Hai all
> I am running a dynamics for protein-dna complex(nucleosome) in vacuum
> 2.I think i am in need of PBC eventhough i dont have solvent. Because in
> a paper it is given that molecules will evaporate wen there is no
> boundary conditions.Is it so?
> 3.Minimisation is ok.Energy is keep on decreasing. But in the case of
> simulation there is sudden increase in the energy and generating
> numbers 99999999.99999. i dont know why?
> I have included my configuration file also. have a look at this.
> timestep 0.000000002 ;# 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
> # Periodic Boundary Conditions
> cellBasisVector1 128. 0. 0.
> cellBasisVector2 0. 199. 0.
> cellBasisVector3 0. 0. 53.
> cellOrigin 56. 100. 8.
> wrapAll on
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 110
> PMEGridSizeY 180
> PMEGridSizeZ 42
> # 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
> # Minimization
> minimize 15000
> reinitvels $temperature
> run 10000 ;# 5ps
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