[Fwd: SMD of titin domain]

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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