Building Gramicidin A
NPT Simulation
The following NAMD configuration file performs the final stage of the
simulation. The langevinDamping parameter has been reduced and the
langevinPistonDecay parameter has been increased to more closely
approximate free dynamics while still maintaining an NPT ensemble.
Options needed only for equilibration have been removed and this is
also an example of continuing a simulation.
nptsim.namd
structure grama.psf
coordinates equil_out.coor
velocities equil_out.vel
extendedSystem equil_out.xsc
parameters par_all27_prot_lipid.inp
parameters par-extraterms.inp
paraTypeCharmm on
outputEnergies 10
outputTiming 100
xstFreq 100
dcdFreq 100
wrapAll on
wrapNearest on
timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
switching on
switchDist 8.5
cutoff 10
pairlistdist 11.5
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 2
Pme on
PmeGridsizeX 32
PmeGridsizeY 32
PmeGridsizeZ 64
exclude scaled1-4
1-4scaling 1.0
# use lighter damping now that system is equilibrated
langevin on
langevinDamping 1
langevinTemp 310
langevinHydrogen no
# use lighter damping now that system is equilibrated
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 310
useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate independently
useConstantRatio yes # fix shape in x-y plane
binaryoutput off
outputname nptsim_out
firsttimestep 20000
run 20000
Submit the job using BioCoRE or "bsub < bptsim.job", the necessary files
were either uploaded for or created by the previous run. The run should
take about 30 minutes once it starts.
nptsim.job
#!/bin/csh
#BSUB -n 8
#BSUB -W 1:00
#BSUB -q workshop
mpirun -np $BSUB_NUMTHREADS /usr/local/apps/chemistry/namd/current/namd2 nptsim.namd > nptsim.log
When the job completes, you can download the trajectory file and
inspect your results.
