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
-- The future is now!
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