From: dora guzman (dguzman_at_uci.edu)
Date: Wed Feb 08 2006 - 17:05:34 CST
attached mail follows:
Hello,
I'm trying to simulate Shulten's work on the muscle protein titin as my
control, as I'm learning how to use NAMD and SMD. However, I can't seem
to get the exact results he's published. My force-extension curves show
the initial signature peak of the mechanical resistance to unfolding of
the parallel beta-strands, but I also observe a significant increase in
force upon further unfolding within the remaining beta-strands. I've
attached the config file for your information. Any input would be
appreciated.
Thanks.
-dg
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Constant Velocity Pulling N- C- Termini of TTN (1fs)
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../commonTTN/ttn_ION.psf
coordinates ../commonTTN/ttn_ION.pdb
# starting SMD from min-eq files
bincoordinates ../commonTTN/ttn_ION_eq5-3.restart.coor
outputName ttn_SMD-0.5-3
set temperature 300
# Continuing a job from the restart files
if {0} {
set inputname myinput
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove "temperature" if use this!
extendedSystem $inputname.xsc
}
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../commonTTN/par_all22_prot.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!
if {0} {
cellBasisVector1 50. 0. 0.
cellBasisVector2 0. 110. 0.
cellBasisVector3 0. 0 50.
cellOrigin 0. 0. 0.
}
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds none ;# all needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 64
}
# Constant Temperature Control
langevin off ;# do not do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
if {0} {
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 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 250
outputPressure 250
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile ../commonTTN/ttn_ION_eq2.ref
fixedAtomsCol B
}
# 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...)
SMD on
SMDFile ../commonTTN/ttn_ION_eq2.ref
SMDk 6
SMDVel 0.0005
SMDDir 0.867 -0.441 0.231
SMDOutputFreq 10
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {0} {
minimize 100
reinitvels $temperature
}
run 500000 ;# timesteps, 500 ps
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