NAMD NVT run configuration capturing lots of position frames for smooth animations

animation_capture.namd

# Obviously, this will need to be modified for the particular situations at hand,
# but capturing every 50 timesteps at 2 fs/step is a good starting point for a
# 30 fps animation.

# Run with the following command line
# charmrun ++remote-shell ssh +p10 $(which namd2) 5eui_nvt.namd | tee 5eui_minimize_log.out

structure          5eui_nvt.psf
coordinates        5eui_nvt.pdb

# Temperature is used in both minimization and NVT steps
set temperature    310  ;# target temperature used several times below

# Set temperature to set velocities for minimization. Comment out for NVT.
# temperature         $temperature    ;# initialize velocities randomly

# continuing a run
# Uncomment these lines to continue run after minimization
# Leave commented out for minimization

set inputname      5eui_minimize          ;# only need to edit this in one place!
binCoordinates     $inputname.restart.coor        ;# coordinates from last run (binary)
binVelocities      $inputname.restart.vel         ;# velocities from last run (binary)

# .xsc not needed here
# extendedSystem	   $inputname.xsc         ;# cell dimensions from last run

firsttimestep      2000                   ;# last step of previous run

# Number of steps is set below, commenting out here
# numsteps           250000                   ;# run stops when this step is reached

outputName         5eui_nvt   ;# base name for output from this run

# The DCD output deserves special mention. It contains every position of the
# atoms that will show up as a frame in the animation. Write to it frequently
# For 90,000 steps (see below) every 50 steps will give us 1800 frames for
# a minute of video. All other logging output will match its frequency.

dcdfreq             50       ;# Write every 50 steps from to the DCD

# Frequency at which to write the files
restartfreq         500     ;# 500 steps = every 1ps. Don't need restart data at every step.
xstFreq             50

# Energies and the computation time estimates aren't needed for animation,
# so they do not need to be written as often. This boosts performance since
# energies are expensive to compute.
outputEnergies      500;     # Energies aren't needed for the animation. Don't compute as often.
outputTiming        500;     # Timing until the end of the run aren't used for the animation.

# Force-Field Parameters
paraTypeCharmm	    on
parameters          par_all36_lipid_prot_carb.prm

# These are specified by CHARMM
exclude             scaled1-4
1-4scaling          1.0
switching           on

# You have some freedom choosing the cutoff
cutoff              12. ;# may use smaller, maybe 10., with PME
switchdist          10. ;# cutoff - 2.

# Promise that atom won't move more than 2A in a cycle
pairlistdist        14. ;# cutoff + 2.

stepspercycle       10   ;# redo pairlists every ten steps

# Integrator Parameters
timestep            2.0  ;# 2 fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1    ;# nonbonded forces every step
fullElectFrequency  2    ;# PME only every other step

# Constant Temperature Control
langevin            on            ;# langevin dynamics
langevinDamping     1.            ;# damping coefficient of 1/ps
langevinTemp        $temperature  ;# random noise at this level
langevinHydrogen    no            ;# don't couple bath to hydrogens

# Periodic Boundary conditions
cellBasisVector1 70.30900001525879 0 0
cellBasisVector2 0 70.30600166320801 0
cellBasisVector3 0 0 61.305999755859375
cellOrigin -6.241292476654053 -16.991411209106445 -17.680774688720703

# Water wrapping
wrapWater           on              ;# wrap water to central cell
wrapAll             on              ;# wrap other molecules too
wrapNearest         off             ;# use for non-rectangular cells

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

# let NAMD determine grid
PMEGridSpacing      1.0

# manually specify grid
#PMEGridSizeX        32  ;# 2^5, close to 31.2
#PMEGridSizeY        45  ;# 3^2 * 5, close to 44.8
#PMEGridSizeZ        54  ;# 2 * 3^3, close to 51.3

# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigid bonds
useFlexibleCell       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, maybe for membrane

langevinPiston        on
langevinPistonTarget  1.01325      ;# pressure in bar -> 1 atm
langevinPistonPeriod  100.         ;# oscillation period around 100 fs
langevinPistonDecay   50.          ;# oscillation decay time of 50 fs
langevinPistonTemp    $temperature ;# coupled to heat bath

# We aren't using fixed atoms in this minimization.
# fixedAtoms          on
# fixedAtomsFile      myfixedatoms.pdb  ;# flags are in this file
# fixedAtomsCol       B                 ;# set beta non-zero to fix an atom

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?

# Do not attempt to minimize the structure. It is already minimized.
# minimize            2000          ;# lower potential energy for 1000 steps

reinitvels          $temperature  ;# since minimization zeros velocities
run  90000          ;# Run 90,000 steps