From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Thu Mar 29 2007 - 13:18:06 CDT
*Regarding the equilibration procedure here is a table that explain the
25 ns preparation, before running 10 ns production under NPAT ensemble:
|---------- kcal/mol/A^2 --------|
*
*
* *
* *Protein* *Lipids* *COM* *Steps*
*
* *
* *non backbone* *backbone* *P* *protein* *small* *large* *huge*
*min1* *NVT* *fixed* *fixed* *100.0* *
* *3,500* *5,000* *15,000*
*heat1* *NV* *fixed* *fixed* *100.0* *
* *20,000* *20,000* *20,000*
*eq1* *NVT* *fixed* *fixed* *100.0* *
* *25,000* *25,000* *25,000*
*annealing* *NVT* *fixed* *fixed* *100.0* *
* *200,000* *200,000* *200,000*
*eq2* *NPAT* *fixed* *fixed* *10.0* *
* *100,000* *100,000* *100,000*
*eq3* *NpgT* *fixed* *fixed* *5.0* *
* *10,000,000* *10,000,000* *15,000,000*
*eq4* *NPAT* *1.0* *50.0* *1.0* *
* *100,000* *100,000* *100,000*
*eq5* *NPAT* *0.5* *20.0* *0.5* *
* *100,000* *100,000* *100,000*
*eq6* *NPAT* *0.0* *5.0* *0.0* *
* *100,000* *100,000* *100,000*
*eq7* *NPAT* *0.0* *1.0* *0.0* *
* *100,000* *100,000* *100,000*
*eq8* *NPAT* *0.0* *0.2* *0.0* *
* *100,000* *100,000* *100,000*
*eq9* *NPAT* *0.0* *0.05* *0.0* *
* *401,500* *400,000* *390,000*
*eq10* *NPAT* *0.0* *0.00* *0.0* *1000.0* *1,250,000*
*1,250,000* *1,250,000*
*
* *
* *
* *
* *
* *
* *
* *
* *
*
*Total ns* *
* *
* *
* *
* *
* *25.00* *25.00* *35.00*
*I have many systems with sizes ~6,000, 13,000, 33,000, or 86,000 atoms.
Sterling, would you explain to me how to do pressure autocorrelation
time calculations.
Another possibility from our discussion is that I am using Multiple
Timesteps, and yet no one confirmed if that could have an effect or not.
My understanding that by activating that method it will only speed up
the process of the integration.
By the way, I had a run for 2.5 ns using Peter's suggestion, and the
results of that run have the same problem as those who use 500 fs decay.
**LangevinPistonPeriod 200.0 ;# fs
LangevinPistonDecay 50.0 ;# fs*
*
Bellow my signature I am posting part of my namd script, just to make
sure that every thing is setup correctly for NPAT ensemble.
Thanks
Morad Alawneh
set Numer_of_Steps 5000000
set Temp 303.15
####################################################################################
# Input Files
structure "../../psfgen/$InputName.psf-old_TRP"
coordinates "../../psfgen/$InputName.pdb-old_TRP"
bincoordinates [concat "../$InputName\_$Process0\.coor"]
binvelocities [concat "../$InputName\_$Process0\.vel"]
parameters "../../psfgen/par_all27_prot_lipid.prm-old_TRP"
paraTypeCharmm on
####################################################################################
# Output Files
outputname $OutputName
binaryoutput yes
DCDfile $OutputName.dcd
DCDfreq 1000
####################################################################################
# Timestep Parameters
numsteps $Numer_of_Steps
timestep 2.0
firsttimestep $FirstTimeStep
####################################################################################
# Simulation Space Partitioning
switching on
switchDist 8.0
cutoff 12.0
pairlistdist 14.0
margin 5.0
pairlistsPerCycle 4
####################################################################################
# Basic Dynamics
exclude scaled1-4
1-4scaling 1.0
seed 2006
rigidBonds all
zeroMomentum yes
####################################################################################
# PME Parameters
PME yes
PMEGridSizeX 64
PMEGridSizeY 64
PMEGridSizeZ 256
PMEInterpOrder 6
####################################################################################
# Multiple Timestep Parameters
fullElectFrequency 2
####################################################################################
# Temperature Control
# Langevin Dynamics Parameters
langevin on
langevinTemp $Temp
langevinDamping 5.0
langevinHydrogen on
####################################################################################
# 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 ;# default
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 200.0 ;# fs
LangevinPistonDecay 50.0 ;# fs
LangevinPistonTemp $Temp*
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