Re: Pressure Discrepancy

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Fri Apr 20 2007 - 06:01:44 CDT

Hi all,

I still say his box size isn't right. He should do as I did to find the "correct" box size.

Richard
 
Richard L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030
rwoodphd_at_yahoo.com

----- Original Message ----
From: Sterling Paramore <paramore_at_hec.utah.edu>
To: Morad Alawneh <alawneh_at_chem.byu.edu>
Cc: namd-l_at_ks.uiuc.edu
Sent: Thursday, April 19, 2007 11:16:04 PM
Subject: Re: namd-l: Pressure Discrepancy

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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