Re: Pressure Discrepancy

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Wed Mar 28 2007 - 13:23:04 CDT

*No, I do not.
I have attached the NAMD script file to those who want to check my the
input parameters.

Thanks

Morad Alawneh
*
Marcos Sotomayor wrote:
>
> Are you using multiple time stepping?
>
> Marcos
>
> On Wed, 28 Mar 2007, Morad Alawneh wrote:
>
>> *There is one suggestion, which is to use NVT ensemble, by having
>> different box sizes and choose the box size that gives you the right
>> pressure. This suggestion is fine if you can use NVT ensemble, which
>> varies the pressure and keeps the box size constant.
>>
>> Unfortunately, this suggestion is not suitable for my case, since I have
>> to use NPAT ensemble.
>>
>> I think there are some bugs in the NAMD algorithms, since I found other
>> two problems. I was not able to constrain the com of my protein around
>> the origin for whatever the force constant I use in both SMD or Free
>> Energy of Conformational Change Calculations.
>>
>> I sent a copy of my notes to James Phillips, NAMD developer, hopping to
>> here back from him soon.
>>
>> Thanks
>>
>> Morad Alawneh
>> **
>> *
>> tamal_at_iitk.ac.in wrote:
>>> I am also finding the same problem.It never relates with our input
>>> pressure.Have you got any reply?.
>>> Thanks for your referred paper in your mail.It is really a
>>> fundamental paper.
>>>
>>> thanks
>>> Tamal Banerjee
>>>
>>>
>>>> *Dear NAMD Developers and users,
>>>>
>>>> I am trying to evaluate the surface tension of my system (a protein
>>>> surrounded by a lipid bilayer in water and salt) using this equation:
>>>> 0.5*Lz*(Pzz - Pt), where
>>>>
>>>> Lz: the box length in z direction, which is the reaction coordinate.
>>>> Pzz: the pressure sensor in z direction
>>>> pt = 0.5*(Pxx + Pyy)
>>>>
>>>> I am using the NPAT ensemble with the following settings in NAMD2.6:
>>>>
>>>> # Langevin Dynamics Parameters
>>>> langevin on
>>>> langevinTemp 303.15
>>>> langevinDamping 5.0
>>>> langevinHydrogen on
>>>> # 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 200.0
>>>> LangevinPistonDecay 500.0
>>>> LangevinPistonTemp 303.15
>>>> # 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
>>>>
>>>> According to the article
>>>> ** ZHANG YH, FELLER SE, BROOKS BR, et al.
>>>> COMPUTER-SIMULATION OF LIQUID/LIQUID INTERFACES .1. THEORY AND
>>>> APPLICATION TO OCTANE/WATER
>>>> <http://apps.isiknowledge.com/WoS/CIW.cgi?SID=2EPNc3mJfLCGDA6hnmm&Func=Abstract&doc=9/5>
>>>>
>>>> JOURNAL OF CHEMICAL PHYSICS 103 (23): 10252-10266 DEC 15 1995 *
>>>> *Pzz should take the value of Pn, which is ~ 1 bar, but when I tested
>>>> its values it had different values.
>>>> If I take the average of those pressure values, they are far away
>>>> from 1
>>>> bar, here is an example:
>>>>
>>>> Pxx Pyy Pzz Pt
>>>> P <P>
>>>> 720.2230 415.1900 -427.7030 567.7070 235.9037
>>>> 235.9037
>>>> 196.3230 577.8960 266.0390 387.1090 346.7525
>>>> 107.5640
>>>> ............... ............... ...............
>>>> ................ ............... .............
>>>> **simulation average: -16.4359 -112.3742 -80.3948
>>>> -54.0773
>>>>
>>>> I know there is a huge fluctuations in pressure, but the average
>>>> values
>>>> should take care of that and be close to 1 bar for Pzz, P, or <P>.
>>>>
>>>> Would you explain to me why do I have this kind of pressure
>>>> discrepancy
>>>> for Pzz, P, or <P>?
>>>>
>>>> Thanks
>>>>
>>>> Morad Alawneh
>>>>
>>>>
>>>> **
>>>>
>>>>
>>>>
>>>> *
>>>>
>>>>
>>>>
>>>
>>>
>>> *****************************************
>>> Tamal Banerjee
>>> Research Scholar
>>> Department of Chemical Engineering
>>> I.I.T Kanpur
>>> Phone: +91-512-2597533 (Lab)
>>> +91-512-2595433 (Residence)
>>> URL: home.iitk.ac.in/~tamal
>>> *****************************************
>>>
>>>
>>
>


# Equilibrate the system under NPAT

set InputName sys
set Process0 equil10
set Process prod
set LastRun 0
set OutputName [concat "$InputName\_$Process"]
#set FixedAtoms fixed.pdb
#set Restraints [concat "restraints_$Process0\.pdb"]
set ESF [concat "../prep/$InputName\_$Process0\.xsc"]
set Numer_of_Steps 5000000
set FirstTimeStep [expr {$Numer_of_Steps*$LastRun}]
set Temp 303.15
set Dist_Temp 303.15
#set Gamma ??.0 ;# dyn/cm
####################################################################################
# Input Files

structure "../psfgen/$InputName.psf"
coordinates "../psfgen/$InputName.pdb"
bincoordinates [concat "../prep/$InputName\_$Process0\.coor"]
binvelocities [concat "../prep/$InputName\_$Process0\.vel"];# use this or
                                                                    ;# temperature
parameters "../psfgen/par_all27_prot_lipid.prm"
paraTypeCharmm on
####################################################################################
# Output Files

outputname $OutputName
binaryoutput yes ;# default
#restartname res_$OutputName ;# produces pdb restart file
#restartfreq 100 ;# generate restart file every N timesteps
DCDfile $OutputName.dcd
DCDfreq 500
####################################################################################
# Standard Output

outputEnergies 100 ;# timesteps between energy output
outputMomenta 100 ;# timesteps between momenta output
outputPressure 100 ;# timesteps between pressure output
outputTiming 100 ;# timesteps between timing output
####################################################################################
# Timestep Parameters

numsteps $Numer_of_Steps ;# run stops when this step is reached
timestep 2.0 ;# fs
firsttimestep $FirstTimeStep ;# use this instead of restart from 0
stepspercycle 20 ;# default
####################################################################################
# Simulation Space Partitioning

switching on
switchDist 8.0
cutoff 12.0
pairlistdist 14.0
margin 2.0
pairlistsPerCycle 4
####################################################################################
# Basic Dynamics

#temperature $Temp ;# use this or binvelocities
exclude scaled1-4 ;# specified by CHARMM
1-4scaling 1.0 ;# specified by CHARMM
seed 2006
rigidBonds all ;# activate ShakeH
rigidTolerance 0.00000001 ;# default
rigidIterations 100 ;# default
useSettle on ;# default
dielectric 1.0 ;# default
COMmotion no ;# default
zeroMomentum yes
####################################################################################
# PME Parameters

PME yes
PMEGridSizeX 64 ;# Should be > 1.5 the box width
PMEGridSizeY 64 ;# Should be > 1.5 the box height
PMEGridSizeZ 256 ;# Should be > 1.5 the box length
PMEInterpOrder 6
####################################################################################
# Multiple Timestep Parameters

fullElectFrequency 2
nonbondedFreq 1
MTSAlgorithm impulse ;# default
longSplitting c1 ;# default
####################################################################################
# Harmonic Constraint Parameters

#constraints on
#consexp 2 ;# default, use only even integers
#consref $Restraints
#conskfile $Restraints
#conskcol B
#selectConstraints on ;# Planer restraint
#selectConstrZ on
####################################################################################
# Fixed Atoms Parameters

#fixedAtoms on
#fixedAtomsForces on ;# keep it off at CP
#fixedAtomsFile $FixedAtoms
#fixedAtomsCol B
####################################################################################
# Temperature Control

# Langevin Dynamics Parameters
langevin on
langevinTemp $Temp
langevinDamping 5.0 ;# /ps
langevinHydrogen on ;# default

# Temperature Coupling Parameters
#tCouple on
#tCoupleTemp $Temp
#tCoupleFile
#tCoupleCol B

# Temperature Rescalling Parameters
#rescaleFreq 50
#rescaleTemp $Temp

# Temperature Reassignment Parameters, usefull for annealing
#reassignFreq 50
#reassignTemp $Temp
#reassignIncr 5.0
#reassignHold $Dist_Temp
####################################################################################
# Boundary Conditions

# Spherical Harmonic Conditions

# Cylindrical Harmonic 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 ;# default
wrapWater on
wrapAll on
wrapNearest off ;# use for non-rectangular cells
extendedSystem $ESF
####################################################################################
# Pressure Control

useGroupPressure yes
useFlexibleCell yes ;# anisotropic cell fluctuations
useConstantRatio no ;# constant shape in x-y plane
useConstantArea yes ;# constant area; constant dimentions in x-y
                                       ;#plane

# Nose-Hoover Langevin Piston Pressure Control
LangevinPiston on
LangevinPistonTarget 1.01325 ;# 1 atm 1.01325 bar
LangevinPistonPeriod 200.0 ;# fs
LangevinPistonDecay 500.0 ;# fs
LangevinPistonTemp $Temp
#SurfaceTensionTarget $Gamma
####################################################################################
# Interactive Molecular Dynamics

IMDon on
IMDport 2006
IMDfreq 1
IMDignore yes
####################################################################################
# Energy Minimization: Conjugate Graidient Parameters

#minimization on
#minTinyStep 0.000001 ;# defalut
#minBabyStep 0.0100 ;# default
####################################################################################
# # Tcl Forces and Analysis
#
# set PDB [concat "../psfgen/$InputName\.pdb"]
# ###----------------
# 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"
####################################################################################

#minimize 5000

run $Numer_of_Steps

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:30 CST