Commit 7fd449a0 authored by Berk Onat's avatar Berk Onat
Browse files

Initial commit for NAMD parser

parents
set temperature 300 ;# target temperature used several times below
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 $temperature
seed 74269
# Constant Temperature Control
#langevin on ;# langevin dynamics
#langevinDamping 1. ;# damping coefficient of 1/ps
#langevinTemp $temperature ;# random noise at this level
#langevinHydrogen no ;# don't couple bath to hydrogens
loweAndersen on
loweAndersenTemp $temperature
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
#langevinPiston on
#langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm
#langevinPistonPeriod 100. ;# oscillation period around 100 fs
#langevinPistonDecay 50. ;# oscillation decay time of 50 fs
#langevinPistonTemp $temperature ;# coupled to heat bath
BerendsenPressure on
BerendsenPressureTarget 1.01325
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 100.
BerendsenPressureFreq 20
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
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This diff is collapsed.
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
This diff is collapsed.
(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
# 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
This diff is collapsed.
This diff is collapsed.
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
This diff is collapsed.
(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0) (3 537 -1 0 4428 1 0 67 0) (9 537 -1 0 4428 1 0 199 0) (27 537 -1 0 4428 1 1 66 0) (2 537 -1 0 4428 1 0 45 0) (6 537 -1 0 4428 1 0 133 0) (18 537 -1 0 4428 1 1 66 0) (54 537 -1 0 4428 1 1 198 0) (4 537 -1 0 4428 1 0 89 0) (12 537 -1 0 4428 1 0 265 0) (36 537 -1 0 4428 1 1 66 0) (108 537 -1 0 4428 1 1 198 0) (3 537 1 0 4428 1 0 78 0) (9 537 1 0 4428 1 0 210 0) (27 537 1 0 4428 1 1 77 0) (2 537 1 0 4428 1 0 56 0) (6 537 1 0 4428 1 0 144 0) (18 537 1 0 4428 1 1 77 0) (54 537 1 0 4428 1 1 209 0) (4 537 1 0 4428 1 0 100 0) (12 537 1 0 4428 1 0 276 0) (36 537 1 0 4428 1 1 77 0) (108 537 1 0 4428 1 1 209 0))
\ No newline at end of file
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