From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jul 30 2010 - 02:11:59 CDT
Hello.
The pressure fluctuates because of the small size of the system.
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node32.html
This is probably normal.
Best regards,
Ajasja
On Thu, Jul 29, 2010 at 21:01, Parisa Akhski
<Parisa.Akhshi_at_chem.queensu.ca>wrote:
>
> Dear NAMD users,
>
> I have minimized a DNA structure and I am doing equilibration by as a set
> of restrained simulations in NPT ensemble. I am setting the pressure by
> using the langevinPiston as below:
>
>
> ## Input files
>
> structure a.psf
> coordinates a.pdb
>
> ########################################################
>
> set temperature 310
> set outputname output
>
> firsttimestep 0
>
>
> # Input
> paraTypeCharmm on
> parameters par_all27_na.prm
> temperature $temperature
>
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
> margin 3.0
>
> # 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
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 49.9 0. 0.
> cellBasisVector2 0. 58.5 0.
> cellBasisVector3 0. 0. 57.4
> cellOrigin 9.96 5.22 7.81
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 45
> PMEGridSizeY 54
> PMEGridSizeZ 54
>
> # 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
>
>
> constraints on
> consexp 2
> consref b.pdb
> conskfile b.pdb
> conskcol B
>
>
> # Output
> outputName $outputname
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Equilibration
>
> numsteps 100000
>
>
> But, the pressure in the output file is very different from what I defined
> (1bar)and is not constant at all. I get negative values which are just
> fluctuating randomly. Any help is really appreciated.
>
> Parisa
>
>
>
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