HrcQb, I41W, Trps inside
Native tetrameric Qb. It is the second time that Trps have been modelled inside the interface. The first time the dimers had been taken apart.
The job was submitted via sbatch using:
#!/bin/tcsh -f /usr/local/namd/charmrun /usr/local/namd/namd2 +p32 +giga +strategy USE_HYPERCUBE ++useip 10.0.0.1 equi.namd >& LOG
The NAMD script was:
# Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel extendedSystem heat_out.xsc parameters par_all27_prot_na.inp paraTypeCharmm on umount /media/usb # # Output files & writing frequency for DCD # and restart files # outputname output/equi_out binaryoutput off restartname output/restart restartfreq 1000 binaryrestart yes dcdFile output/equi_out.dcd dcdFreq 200 DCDunitcell yes # # Frequencies for logs and the xst file # outputEnergies 20 outputTiming 200 xstFreq 200 # # Timestep & friends # timestep 2.0 stepsPerCycle 20 nonBondedFreq 2 fullElectFrequency 4 # # Simulation space partitioning # switching on switchDist 10 cutoff 12 pairlistdist 14.5 # # Basic dynamics # COMmotion no dielectric 1.0 exclude scaled1-4 1-4scaling 1.0 rigidbonds all # # Particle Mesh Ewald parameters. # Pme on PmeGridsizeX 128 # <===== CHANGE ME PmeGridsizeY 96 # <===== CHANGE ME PmeGridsizeZ 64 # <===== CHANGE ME Pmeprocessors 16 # # Periodic boundary things # wrapWater on wrapNearest on wrapAll on # # Langevin dynamics parameters # langevin on langevinDamping 1 langevinTemp 320 # <===== Check me langevinHydrogen on langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 320 # <===== Check me useGroupPressure yes firsttimestep 120000 # <===== CHANGE ME run 100000000 ;# <===== CHANGE ME
HrcQb, I41W, Trps on the outside
The job was submitted with
nohup using:
#!/bin/tcsh -f nohup /usr/local/namd/charmrun /usr/local/namd/namd2 +p28 +giga ++useip 10.0.0.1 equi.namd >& LOG &
The NAMD script was:
# Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel extendedSystem heat_out.xsc parameters par_all27_prot_na.inp paraTypeCharmm on # # Output files & writing frequency for DCD # and restart files # outputname output/equi_out binaryoutput off restartname output/restart restartfreq 1000 binaryrestart yes dcdFile output/equi_out.dcd dcdFreq 200 DCDunitcell yes # # Frequencies for logs and the xst file # outputEnergies 20 outputTiming 200 xstFreq 200 # # Timestep & friends # timestep 2.0 stepsPerCycle 20 nonBondedFreq 2 fullElectFrequency 4 # # Simulation space partitioning # switching on switchDist 10 cutoff 12 pairlistdist 14.5 # # Basic dynamics # COMmotion no dielectric 1.0 exclude scaled1-4 1-4scaling 1.0 rigidbonds all # # Particle Mesh Ewald parameters. # Pme on PmeGridsizeX 128 # <===== CHANGE ME PmeGridsizeY 80 # <===== CHANGE ME PmeGridsizeZ 64 # <===== CHANGE ME Pmeprocessors 16 # # Periodic boundary things # wrapWater on wrapNearest on wrapAll on # # Langevin dynamics parameters # langevin on langevinDamping 1 langevinTemp 320 # <===== Check me langevinHydrogen on langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 200 langevinPistonDecay 100 langevinPistonTemp 320 # <===== Check me useGroupPressure yes firsttimestep 120000 # <===== CHANGE ME run 100000000 ;# <===== CHANGE ME
user/vasiliki_e_fadouloglou/projects/hrcqb_i41w.txt · Last modified: 2009/02/16 10:34 (external edit)
