RE: [Fwd: SMD of titin domain]

From: Mu Gao (mugao_at_ks.uiuc.edu)
Date: Wed Feb 08 2006 - 19:23:29 CST

Dear Dora,

 

Since you are pulling the protein at high velocity of 0.05A/ps, it is
possible that minor force peaks arise after the major unfolding event.
However, these peaks are significant lower than the major signature peak
force. As you slow down the pulling velocity, you will see force decreasing
and minor force peaks may disappear.

 

Hope this helps,

 

Mu Gao

 

  _____

From: JC Gumbart [mailto:gumbart_at_ks.uiuc.edu]
Sent: Wednesday, February 08, 2006 5:26 PM
To: Mu Gao
Cc: Eric H. Lee
Subject: Fwd: namd-l: [Fwd: SMD of titin domain]

 

This was sent to the namd list; I thought you guys might want to offer
input.

JC

Begin forwarded message:

From: dora guzman <dguzman_at_uci.edu>
Date: February 8, 2006 5:05:34 PM CST
To: namd <namd-l_at_ks.uiuc.edu>
Subject: namd-l: [Fwd: SMD of titin domain]

From: dora guzman <dguzman_at_uci.edu>
Date: February 8, 2006 4:56:36 PM CST
To: majordomo_at_ks.uiuc.edu
Subject: SMD of titin domain

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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