NAMD Equil Config

From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Thu Sep 22 2016 - 07:24:53 CDT

Hello All,

I am attempting to minimize and equilibrate the integrin alphaVbeta6 in
order to run constant force simulations. I can't seem to get the simulation
parameters right in order to do what I want, and I was wondering if there
was any chance someone could look at my equilibration file to see if my
setup is right.

The equilibration file I have copied into this email is one of several
equilibration steps I used to equilibrate the integrin molecule. Before my
equilibration, I ran a minimization of the molecule in a water box. After
all of my equil simulations, I checked the rmsd trajectory and seemed to
get a conformationally stable molecule. However, when I ran a constant
force simulation, I ran into a problem in which the molecules to which the
force is applied fly off at high speeds (no matter how large or small the
force). I am wondering if anyone can see any glaring issues in the equil
file that could potentially cause problems?

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Equilibration of alphVbeta3 after minimization
# Shorter simulations so dcd can be analyzed

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure ../alphaVbeta6_wb.psf
coordinates ../alphaVbeta6_wb.pdb

set temperature 310
set outputname beta6_equil_1

# Continuing a job from the restart files
if {1} {
set inputname ../minimization/beta6_min_fixed_protein
binCoordinates $inputname.restart.coor
#binVelocities $inputname.restart.vel
extendedSystem $inputname.xsc
}

firsttimestep 100000

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

# Input
paraTypeCharmm on
parameters ../par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

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

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

# Periodic Boundary Conditions
cellBasisVector1 121 0.0 0.0
cellBasisVector2 0.0 93 0.0
cellBasisVector3 0.0 0.0 57.5
cellOrigin 20.045 -30.903 25.591

wrapWater on
wrapAll on
wrapNearest off

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 200
outputPressure 200

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

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

# Minimization
#minimize 10000
reinitvels $temperature

run 10000 ;# .02 ns, now at 0 ns

If there are any questions about what I did or why I did it, I would be
happy to explain. I really appreciate your help!

Thank You,

Jack

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