Now that we've built all of our input files we can finally run NAMD. The protocol will consist of the following stages:
  1. Minimization with fixed backbone atoms.
  2. Minimization with restrained carbon alpha atoms.
  3. Langevin dynamics with restraints.
  4. Constant pressure with restraints.
  5. Constant pressure without restraints.
  6. Constant pressure with reduced damping coefficients.
The following NAMD configuration file performs all but the last stage. Run times have been reduced to finish the run as quickly as possible. A real production simulation might equilibrate for 1 ns.

structure 	grama.psf
coordinates 	grama.pdb
temperature	0
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

cellBasisVector1	30.00	00.00 	00.00
cellBasisVector2	15.00	25.98	00.00
cellBasisVector3	00.00	00.00	64.00
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 5

Pme		on
PmeGridsizeX	32
PmeGridsizeY	32
PmeGridsizeZ	64	

exclude		scaled1-4
1-4scaling	1.0

fixedAtoms		on
fixedAtomsForces	on
fixedAtomsFile		fix_backbone.pdb
fixedAtomsCol		B

constraints	on
consRef		restrain_ca.pdb
consKFile	restrain_ca.pdb
consKCol	B

langevin		on
langevinDamping		10
langevinTemp		310
langevinHydrogen	no

langevinPiston		on
langevinPistonTarget	1.01325
langevinPistonPeriod	200
langevinPistonDecay	100
langevinPistonTemp	310

useGroupPressure	yes	# smaller fluctuations
useFlexibleCell		yes	# allow dimensions to fluctuate independently
useConstantRatio	yes	# fix shape in x-y plane

binaryoutput	off
outputname	equil_out

# run one step to get into scripting mode
minimize 0

# turn off until later
langevinPiston	off

# minimize nonbackbone atoms
minimize 1000
output min_fix

# min all atoms
fixedAtoms	off
minimize 1000
output min_all

# heat with CAs restrained
# langevin	on
run 3000
output heat

# equilibrate volume with CAs restrained
langevinPiston	on
run 5000
output equil_ca

# equilibrate volume without restraints
constraintScaling	0
run 10000

The following files required by NAMD may be found in the temporary working directory used by VMD for this run (VMD's current working directory, most likely C:\Temp\vmd_... on Windows or /usr/tmp/vmd_... on unix):
  • grama.psf (created)
  • grama.pdb (created)
  • fix_backbone.pdb (created)
  • restrain_ca.pdb (created)
  • par_all27_prot_lipid.inp (downloaded)
  • par-extraterms.inp (downloaded)
  • equil.namd (downloaded)
  • equil.job (downloaded)
  • nptsim.namd (downloaded, for next step)
  • nptsim.job (downloaded, for next step)
These files must be copied to your training account on modi4.ncsa.uiuc.edu using one of the secure file transfer protocols supported by NCSA, i.e., scp or kerberized ftp.

It is now time to submit the job to the queue. If you are not using BioCoRE you will need to ssh to modi4 and run "bsub < equil.job"; the "bjobs" command can be used to monitor the progress of your job. This file, shown below, requests 8 cpus on the workshop queue for one hour. Once the job starts, the actual run should take around 40 minutes and you can monitor progress with the command "tail -f equil.log".

#BSUB -n 8
#BSUB -W 1:00
#BSUB -q workshop

mpirun -np $BSUB_NUMTHREADS /usr/local/apps/chemistry/namd/current/namd2 equil.namd > equil.log

In BioCoRE, you would use the workbench job submission tool to first create an account on the NCSA Origin, and then submit a NAMD job to the workshop queue. BioCoRE job submission should be self explanatory.

While your job waits in the queue and runs, you can explore the features of VMD. You can download the equil_out.dcd trajectory file at any time and view your run in VMD. The different stages of minimization and equilibration should be visually apparent.

The following will download and display a precalculated trajectory for both this and the following simulation stage, and you can inspect additional files manually from this directory.

Run this step!     Continue

mol delete all
menu animate on
mol load psf grama.psf pdb grama.pdb
animate read dcd equil_out.dcd
animate read dcd nptsim_out.dcd