Would my simulation setting affect the result? About the parameter "fixedAtomsForces"

From: wayj86 wayj86 (wayj86_at_gmail.com)
Date: Fri Aug 07 2009 - 05:51:42 CDT

Dear all,

I wanted to do minimization and equilibration with the following steps:
(1) Minimized and equilibrated the water with the protein fixed for a short
time;
(2) Further Minimized and equilibrated the whole system with the protein
free to move for more than 5ns.

Here is my configuration file for the first step:
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure 1.psf
coordinates 1.pdb
outputName 1_fix

set temperature 310

# Continuing a job from the restart files
if {0} {
set inputname myinput
Coordinates $inputname.restart.coor
velocities $inputname.restart.vel ;# remove the "temperature"
entry if you
extendedSystem $inputname.xsc
}

firsttimestep 0
binaryoutput no
restartfreq 500 ;# 500steps = every 1ps
restartname 1_fix_res
restartsave no
Binaryrestart yes

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!

cellBasisVector1 95.071 0.0 0.0 #x轴
cellBasisVector2 0.0 77.295 0.0 #y轴
cellBasisVector3 0.0 0.0 80.351 #z轴
cellOrigin 17.398 5.088 -3.404 #initial coordinates

wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 13.
switching on
switchdist 10.
pairlistdist 15

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME (for full-system periodic electrostatics)

PME yes
PMEGridSpacing 1

# Constant Temperature Control
if {1} {
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
}

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
}

DCDfile 1_fix.dcd
dcdfreq 500
XSTfile 1_fix.xst
XSTfreq 500

outputEnergies 100
outputPressure 100
outputtiming 200

# Fixed Atoms Constraint
if {1} {
fixedAtomsForces yes
fixedAtoms on
fixedAtomsFile 1.fix
fixedAtomsCol O
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon on
IMDport 3000 ;# port number (enter it in VMD)
IMDfreq 1 ;# send every 1 frame
IMDwait no ;# wait for VMD to connect before running?
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
if {1} {
minimize 5000
reinitvels $temperature
}

run 20000

According to the namd user's guide, seems that I should leave
"fixedAtomsForces" off when using constant pressure if the coordinates of the
fixed atoms have not been minimized, but I forgot to do this. So I want to
ask, In this case would my simulation setting affect the result? Althought I
did't observe any error in the following simualtion. Thank you.

Stanley
Biomechanics institute
S.C.U.T
China

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The future is now!

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