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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