AdAA conf file

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## JOB DESCRIPTION                                         ##
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# Minimization and equilibration of
# ['A', 'dA', 'A'] in a 15 angstrom water box

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## ADJUSTABLE PARAMETERS                                   ##
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structure          AdAA_wb.psf
coordinates        AdAA_wb.pdb

# Periodic boundary conditions - saved in separate file.
cellBasisVector1 40.277000427246094 0 0
cellBasisVector2 0 34.85300064086914 0
cellBasisVector3 0 0 34.757999420166016
cellOrigin 0.29497894644737244 0.5287485122680664 0.13249140977859497

firsttimestep 0

set outputname     AdAA

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## SIMULATION PARAMETERS                                   ##
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# Input
paraTypeCharmm      on
parameters /users/travis/.charmm/par_all36_prot.prm
parameters /users/travis/.charmm/par_all36_carb.prm
parameters /users/travis/.charmm/par_all36_lipid.prm
parameters /users/travis/.charmm/par_all35_ethers.prm
parameters /users/travis/.charmm/par_all36_na.prm
parameters /users/travis/.charmm/par_all36_cgenff.prm
parameters /users/travis/.charmm/toppar_water_ions_namd.str
parameters /users/travis/.charmm/toppar_all36_prot_c36_d_aminoacids.str

# Force-Field Parameters
margin 2
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
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

wrapAll             on

# 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

# Output
outputName          $outputname

restartfreq         100     ;# 100steps = every 200fs
file mkdir $outputname
dcdfreq             2000
outputEnergies      5000
outputPressure      5000

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## EXECUTION SCRIPT                                        ##
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# Minimization

temperature 298
set temperature 298
langevinTemp $temperature
langevinPistonTemp $temperature

minimize            500

run 5000000 ;# 10ns