Commit 7fd449a0 authored by Berk Onat's avatar Berk Onat
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Initial commit for NAMD parser

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# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
450 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
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cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0
coordinates apoa1.pdb
temperature 300
seed 74269
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
structure apoa1.psf
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
fullElectFrequency 4
numsteps 500
outputtiming 20
outputname apoa1-out
outputEnergies 20 # Energy output frequency
restartfreq 50 # Restart file frequency
DCDfreq 100 # Trajectory file frequency
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REMARKS Additional POPC parameters guessed by Jim Phillips
REMARKS FILENAME="par_all22_popc.xplor"
ANGLE CEL1 CEL1 CTL2 48.00 124.00 ! JCP guess 3/97
ANGLE CEL1 CTL2 CTL2 32.00 112.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 CTL2 0.5000 3 0.00 ! JCP guess 3/97
DIHEDRAL HAL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 HAL 0.1200 3 0.00 ! JCP guess 3/97
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BPTI Interactive Simulation
First start NAMD with bpti.namd, then start VMD as "vmd -e bpti.vmd" to
connect and view the simulation. You may need to edit the command
"imd connect localhost 3111" with the correct hostname, or just type
the correct version in the VMD console.
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mol load psf bpti.psf pdb bpti.pdb
imd connect localhost 3111
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