From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Thu Apr 19 2007 - 22:16:04 CDT
What did the decorrelation time for Pzz end up being in your system?
And what confidence interval are you reporting the standard error at?
Also, you shouldn't necessarily expect the average total pressure to
hit 1 bar exactly (only the zz component) since you used constant area.
-Sterling
On Apr 19, 2007, at 3:05 PM, Morad Alawneh wrote:
> Dear all,
>
> I have here new results to show the pressure problem:
> <Pzz> (bar) = 10.93 (+/- 5.75 SE) (+/- 575.24 SD)
> <P> (bar) = -33.18 (+/- 3.61 SE) (+/- 361.23 SD)
> <V> (A^-3) = 119800.89 (+/- 4.73 SE) (+/- 473.10 SD)
>
> The results show stable average values but away from the target
> pressure, which I conclude something is not right about pressure
> and any quantity related to pressure should not be trusted until
> this problem be figured out.
>
> The results were for 10 ns NPAT simulation under the following
> conditions:
>
> paraTypeCharmm on
> ######################################################################
> ##############
> # Timestep Parameters
>
> numsteps $Numer_of_Steps
> timestep 2.0
> firsttimestep $FirstTimeStep
> stepspercycle 20
> ######################################################################
> ##############
> # Simulation Space Partitioning
>
> switching on
> switchDist 8.0
> cutoff 12.0
> pairlistdist 14.0
> margin 2.0
> pairlistsPerCycle 4
> ######################################################################
> ##############
> # Basic Dynamics
>
> #temperature $Temp
> exclude scaled1-4
> 1-4scaling 1.0
> seed 2006
> rigidBonds all
> rigidTolerance 0.00000001
> rigidIterations 100
> useSettle on
> dielectric 1.0
> COMmotion no
> zeroMomentum yes
> ######################################################################
> ##############
> # PME Parameters
>
> PME yes
> PMEGridSizeX 64
> PMEGridSizeY 64
> PMEGridSizeZ 128
> PMEInterpOrder 6
> ######################################################################
> ##############
> # # Multiple Timestep Parameters
> #
> # fullElectFrequency 2
> # nonbondedFreq 1
> # MTSAlgorithm impulse
> # longSplitting c1
> ######################################################################
> ##############
> # Temperature Control
>
> # Langevin Dynamics Parameters
> langevin on
> langevinTemp $Temp
> langevinDamping 5.0 ;# /ps
> langevinHydrogen on ;# default
> ######################################################################
> ##############
> # Boundary Conditions
>
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 40.0 00.0 00.0
> cellBasisVector2 00.0 40.0 00.0
> cellBasisVector3 00.0 00.0 90.0
> cellOrigin 0.0 0.0 0.0
> wrapWater on
> wrapAll on
> wrapNearest off
> extendedSystem $ESF
> ######################################################################
> ##############
> # Pressure Control
>
> useGroupPressure yes
> useFlexibleCell yes
> useConstantRatio no
> useConstantArea yes
>
> # Nose-Hoover Langevin Piston Pressure Control
> LangevinPiston on
> LangevinPistonTarget 1.01325 ;# 1 atm 1.01325 bar
> LangevinPistonPeriod 1000.0
> LangevinPistonDecay 100.0
> LangevinPistonTemp $Temp
> #SurfaceTensionTarget $Gamma
> ######################################################################
> ##############
> # Tcl Forces and Analysis
>
> set PDB [concat "../../psfgen/$InputName\.pdb-old_TRP"]
> ###----------------
> set SelSegID1 {GA1}
> set SelSegID2 {GA2}
> set SelSegID3 {}
> set SelSegID4 {}
> ###----------------
> set Protein_Center [list 0.0 0.0 0.0]
> ###----------------
> tclForces on
> tclForcesScript "../../psfgen/restraints.tcl"
> ######################################################################
> ##############
>
> Morad Alawneh
>
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