Building Gramicidin A
Equilibration
Now that we've built all of our input files we can finally run NAMD. The protocol will consist of the following stages:- Minimization with fixed backbone atoms.
- Minimization with restrained carbon alpha atoms.
- Langevin dynamics with restraints.
- Constant pressure with restraints.
- Constant pressure without restraints.
- Constant pressure with reduced damping coefficients.
equil.namd 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 10000The 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)
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".
equil.job #!/bin/csh #BSUB -n 8 #BSUB -W 1:00 #BSUB -q workshop mpirun -np $BSUB_NUMTHREADS /usr/local/apps/chemistry/namd/current/namd2 equil.namd > equil.logIn 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
view_sample.vmd 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
