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

Initial commit for NAMD parser

parents
# 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
400 108.8612 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
Running on 1 processors: ./namd2 apoa1-traj-vel/apoa1.namd
charmrun> /usr/bin/setarch x86_64 -R mpirun -np 1 ./namd2 apoa1-traj-vel/apoa1.namd
Charm++> Running on MPI version: 3.1
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 1
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.8.0-beta1-154-g07b6831
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (28-way SMP).
Charm++> cpu topology info is gathered in 0.001 seconds.
Info: NAMD 2.12 for Linux-x86_64-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60800 for mpi-linux-x86_64
Info: Built Mon May 15 16:08:39 BST 2017 by essmpc on mnf145
Info: 1 NAMD 2.12 Linux-x86_64-MPI 1 mnf145 essmpc
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00358593 s
Info: 197.551 MB of memory in use based on /proc/self/stat
Info: Configuration file is apoa1-traj-vel/apoa1.namd
Info: Changed directory to apoa1-traj-vel
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 500
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 108.861 0 0
Info: PERIODIC CELL BASIS 2 0 108.861 0
Info: PERIODIC CELL BASIS 3 0 0 77.758
Info: PERIODIC CELL CENTER 0 0 0
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME apoa1-out.dcd
Info: DCD FREQUENCY 20
Info: DCD FIRST STEP 20
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: VELOCITY DCD FILENAME apoa1-out.veldcd
Info: VELOCITY DCD FREQUENCY 50
Info: VELOCITY DCD FIRST STEP 50
Info: FORCE DCD FILENAME apoa1-out.forcedcd
Info: FORCE DCD FREQUENCY 100
Info: FORCE DCD FIRST STEP 100
Info: OUTPUT FILENAME apoa1-out
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME apoa1-out.restart
Info: RESTART FREQUENCY 100
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16
Info: ENERGY OUTPUT STEPS 20
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 20
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 108 108 80
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.12_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.12_Linux-x86_64-MPI.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 74269
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB apoa1.pdb
Info: STRUCTURE FILE apoa1.psf
Info: PARAMETER file: XPLOR format! (default)
Info: PARAMETERS par_all22_prot_lipid.xplor
Info: PARAMETERS par_all22_popc.xplor
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 177 BONDS
Info: 435 ANGLES
Info: 446 DIHEDRAL
Info: 45 IMPROPER
Info: 0 CROSSTERM
Info: 83 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.848095
Info: Reading pdb file apoa1.pdb
Info: TIME FOR READING PDB FILE: 0.162353
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 92224 ATOMS
Info: 70660 BONDS
Info: 74136 ANGLES
Info: 74130 DIHEDRALS
Info: 1402 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 1568 DIHEDRALS WITH MULTIPLE PERIODICITY (BASED ON PSF FILE)
Info: 276669 DEGREES OF FREEDOM
Info: 32992 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 32992 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 553785 amu
Info: TOTAL CHARGE = -14 e
Info: MASS DENSITY = 0.997951 g/cm^3
Info: ATOM DENSITY = 0.100081 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 1.03563 s, 223.355 MB of memory in use
Info: Startup phase 0 took 0.000569645 s, 223.355 MB of memory in use
Info: ADDED 218698 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.101191 s, 245.375 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-23 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.40436e-16 AT 11.9138
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.10282e-22 AT 11.9138
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.56912e-15 AT 11.9138
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-32 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-15 AT 11.9138
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00105669 s, 245.375 MB of memory in use
Info: Startup phase 3 took 4.50881e-05 s, 245.375 MB of memory in use
Info: Startup phase 4 took 0.000313716 s, 245.375 MB of memory in use
Info: Startup phase 5 took 4.16632e-05 s, 245.375 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00117959 0.0289175 0.0202933
Info: LARGEST PATCH (56) HAS 718 ATOMS
Info: TORUS A SIZE 1 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0642078 s, 264.344 MB of memory in use
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 7 took 0.00291433 s, 267.992 MB of memory in use
Info: Startup phase 8 took 5.87092e-05 s, 267.992 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.000172131 s, 267.992 MB of memory in use
Info: CREATING 2885 COMPUTE OBJECTS
Info: Startup phase 10 took 0.00898105 s, 270.664 MB of memory in use
Info: Startup phase 11 took 6.46459e-05 s, 270.664 MB of memory in use
Info: Startup phase 12 took 0.000458768 s, 288.965 MB of memory in use
Info: Finished startup at 1.21571 s, 288.965 MB of memory in use
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 12352.4560 14603.1480 4549.0710 48.1064 -362073.7646 24229.5343 0.0000 0.0000 82752.2738 -223539.1752 301.0300 -306291.4489 -223524.8478 301.0300 -2568.6725 -3582.2555 921491.4634 -2568.6725 -3582.2555
LDB: ============= START OF LOAD BALANCING ============== 46.3413
LDB: ============== END OF LOAD BALANCING =============== 46.3414
LDB: =============== DONE WITH MIGRATION ================ 46.3417
TIMING: 20 CPU: 49.6107, 2.25059/step Wall: 49.6107, 2.25059/step, 0.300079 hours remaining, 486.492188 MB of memory in use.
ENERGY: 20 17965.5059 22054.9969 5321.8173 125.9640 -348206.1515 31862.6111 0.0000 0.0000 47960.4282 -222914.8282 174.4669 -270875.2564 -223082.7607 180.4931 -133.8115 -346.5459 921491.4634 -1678.6248 -1681.3448
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 20
The last position output (seq=20) takes 0.014 seconds, 486.492 MB of memory in use
TIMING: 40 CPU: 94.3071, 2.23482/step Wall: 94.3071, 2.23482/step, 0.28556 hours remaining, 491.785156 MB of memory in use.
ENERGY: 40 18175.3607 23091.9465 5712.9374 193.7351 -348398.4383 30569.2891 0.0000 0.0000 47793.1195 -222862.0500 173.8582 -270655.1696 -222794.4436 164.0042 -3285.9428 -815.4642 921491.4634 26.5057 102.4289
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 40
The last position output (seq=40) takes 0.002 seconds, 491.785 MB of memory in use
OPENING VELOCITY DCD FILE
WRITING VELOCITIES TO DCD FILE AT STEP 50
The last velocity output (seq=50) takes 0.016 seconds, 497.211 MB of memory in use
TIMING: 60 CPU: 138.957, 2.23249/step Wall: 138.957, 2.23249/step, 0.27286 hours remaining, 500.781250 MB of memory in use.
ENERGY: 60 23449.5632 23017.6822 5743.3644 198.4364 -341915.2511 25462.3565 0.0000 0.0000 41666.5932 -222377.2554 151.5716 -264043.8485 -222570.6179 157.8443 -5200.1105 -1391.6025 921491.4634 -1160.9392 -1232.5549
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 60
The last position output (seq=60) takes 0.001 seconds, 500.781 MB of memory in use
TIMING: 80 CPU: 183.516, 2.22796/step Wall: 183.516, 2.22796/step, 0.259929 hours remaining, 501.101562 MB of memory in use.
ENERGY: 80 23193.1683 21560.0612 5781.8893 195.6591 -338486.0883 23496.1343 0.0000 0.0000 41930.4061 -222328.7698 152.5313 -264259.1759 -222421.6003 158.7193 -3928.2140 -2382.1056 921491.4634 -1641.5982 -1681.4280
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 80
The last position output (seq=80) takes 0.001 seconds, 501.102 MB of memory in use
LDB: ============= START OF LOAD BALANCING ============== 224.778
LDB: ============== END OF LOAD BALANCING =============== 224.778
LDB: =============== DONE WITH MIGRATION ================ 224.779
Info: Initial time: 1 CPUs 2.23432 s/step 25.8602 days/ns 515.223 MB memory
TIMING: 100 CPU: 228.032, 2.22581/step Wall: 228.032, 2.22581/step, 0.247313 hours remaining, 515.222656 MB of memory in use.
ENERGY: 100 23587.3021 20475.3730 5773.0376 205.1509 -335896.4624 22125.7987 0.0000 0.0000 41455.8051 -222273.9950 150.8048 -263729.8002 -222326.1725 155.8717 -2788.3919 -2294.3880 921491.4634 -2315.9843 -2139.9314
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 100
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 100
WRITING COORDINATES TO RESTART FILE AT STEP 100
FINISHED WRITING RESTART COORDINATES
The last position output (seq=100) takes 0.025 seconds, 517.332 MB of memory in use
WRITING VELOCITIES TO DCD FILE AT STEP 100
WRITING VELOCITIES TO RESTART FILE AT STEP 100
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=100) takes 0.025 seconds, 517.332 MB of memory in use
OPENING FORCE DCD FILE
WRITING FORCES TO DCD FILE AT STEP 100
The last force output (seq=100) takes 0.015 seconds, 517.332 MB of memory in use
LDB: ============= START OF LOAD BALANCING ============== 269.319
LDB: ============== END OF LOAD BALANCING =============== 269.319
LDB: =============== DONE WITH MIGRATION ================ 269.32
TIMING: 120 CPU: 272.54, 2.22539/step Wall: 272.54, 2.22539/step, 0.234902 hours remaining, 517.332031 MB of memory in use.
ENERGY: 120 23278.7483 18843.5009 5721.1112 217.5091 -334559.3222 21317.8986 0.0000 0.0000 42838.0030 -222342.5511 155.8329 -265180.5541 -222260.9694 157.8174 -4802.3839 -2609.8233 921491.4634 -2372.3436 -2326.0161
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 120
The last position output (seq=120) takes 0.001 seconds, 517.332 MB of memory in use
TIMING: 140 CPU: 316.92, 2.21897/step Wall: 316.92, 2.21897/step, 0.221897 hours remaining, 517.332031 MB of memory in use.
ENERGY: 140 20992.5977 17997.1579 5722.1741 192.2140 -333726.9442 21127.4061 0.0000 0.0000 45144.2514 -222551.1431 164.2224 -267695.3945 -222224.0359 156.6847 -5617.7627 -3080.3638 921491.4634 -2486.4081 -2707.4110
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 140
The last position output (seq=140) takes 0.001 seconds, 517.332 MB of memory in use
WRITING VELOCITIES TO DCD FILE AT STEP 150
The last velocity output (seq=150) takes 0.001 seconds, 517.332 MB of memory in use
TIMING: 160 CPU: 361.25, 2.21654/step Wall: 361.25, 2.21654/step, 0.20934 hours remaining, 517.332031 MB of memory in use.
ENERGY: 160 21093.2843 18859.3047 5717.0749 174.4916 -333735.9155 20833.5472 0.0000 0.0000 44515.8597 -222542.3531 161.9365 -267058.2128 -222175.6784 157.1304 -3202.8705 -2752.7603 921491.4634 -2662.6392 -2774.5671
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 160
The last position output (seq=160) takes 0.001 seconds, 517.332 MB of memory in use
TIMING: 180 CPU: 405.51, 2.21296/step Wall: 405.51, 2.21296/step, 0.196707 hours remaining, 517.332031 MB of memory in use.
ENERGY: 180 19770.2943 19384.7964 5738.8341 156.9935 -334084.3523 21065.2916 0.0000 0.0000 45324.2215 -222643.9209 164.8771 -267968.1424 -222142.6342 159.0530 -2684.8629 -2671.3561 921491.4634 -3067.8718 -2853.3729
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 180
The last position output (seq=180) takes 0.001 seconds, 517.332 MB of memory in use
LDB: ============= START OF LOAD BALANCING ============== 446.529
LDB: ============== END OF LOAD BALANCING =============== 446.529
LDB: =============== DONE WITH MIGRATION ================ 446.53
Info: Initial time: 1 CPUs 2.21704 s/step 25.6602 days/ns 522.258 MB memory
TIMING: 200 CPU: 449.738, 2.21143/step Wall: 449.738, 2.21143/step, 0.184286 hours remaining, 522.257812 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 200 21073.6836 18595.6349 5711.8747 190.0258 -334670.2810 21209.9246 0.0000 0.0000 45319.1603 -222569.9770 164.8586 -267889.1374 -222114.5243 159.3415 -5241.8524 -2703.6812 921491.4634 -2833.0374 -2725.7982
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 200
WRITING COORDINATES TO RESTART FILE AT STEP 200
FINISHED WRITING RESTART COORDINATES
The last position output (seq=200) takes 0.026 seconds, 522.258 MB of memory in use
WRITING VELOCITIES TO DCD FILE AT STEP 200
WRITING VELOCITIES TO RESTART FILE AT STEP 200
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=200) takes 0.025 seconds, 522.258 MB of memory in use
WRITING FORCES TO DCD FILE AT STEP 200
The last force output (seq=200) takes 0.002 seconds, 522.258 MB of memory in use
TIMING: 220 CPU: 493.956, 2.21091/step Wall: 493.956, 2.21091/step, 0.171959 hours remaining, 522.257812 MB of memory in use.
ENERGY: 220 21580.9144 19260.1136 5743.1672 189.1021 -335473.8432 21655.3183 0.0000 0.0000 44539.5741 -222505.6536 162.0227 -267045.2277 -222092.6289 160.6373 -5898.3513 -2876.6578 921491.4634 -2490.1050 -2667.0269
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 220
TIMING: 240 CPU: 538.058, 2.20509/step Wall: 538.058, 2.20509/step, 0.159256 hours remaining, 522.257812 MB of memory in use.
ENERGY: 240 22861.0421 20119.9134 5760.6910 171.4213 -335766.3625 21854.4253 0.0000 0.0000 42641.4776 -222357.3920 155.1180 -264998.8695 -222074.0953 160.4824 -3844.9086 -2568.3896 921491.4634 -2527.3782 -2611.4330
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 240
WRITING VELOCITIES TO DCD FILE AT STEP 250
The last velocity output (seq=250) takes 0.001 seconds, 522.258 MB of memory in use
TIMING: 260 CPU: 582.119, 2.20305/step Wall: 582.119, 2.20305/step, 0.14687 hours remaining, 522.257812 MB of memory in use.
ENERGY: 260 22744.9543 19188.2462 5675.1875 191.0393 -336169.7730 21924.7891 0.0000 0.0000 44083.4306 -222362.1259 160.3634 -266445.5564 -222069.6815 161.4987 -3407.4796 -2810.9878 921491.4634 -2776.7403 -2667.0012
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 260
TIMING: 280 CPU: 626.121, 2.2001/step Wall: 626.121, 2.2001/step, 0.13445 hours remaining, 522.257812 MB of memory in use.
ENERGY: 280 22859.3231 19458.4367 5670.0026 185.3899 -336752.6631 22145.1351 0.0000 0.0000 44066.7340 -222367.6417 160.3027 -266434.3757 -222073.4245 161.6460 -4286.3895 -2748.0547 921491.4634 -2693.2716 -2613.5244
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 280
LDB: ============= START OF LOAD BALANCING ============== 666.93
LDB: ============== END OF LOAD BALANCING =============== 666.93
LDB: =============== DONE WITH MIGRATION ================ 666.931
Info: Initial time: 1 CPUs 2.20362 s/step 25.5049 days/ns 522.258 MB memory
TIMING: 300 CPU: 670.101, 2.19902/step Wall: 670.101, 2.19902/step, 0.122168 hours remaining, 522.257812 MB of memory in use.
ENERGY: 300 21869.9883 20174.1888 5731.6695 182.6816 -337209.9028 22385.4777 0.0000 0.0000 44423.7997 -222442.0972 161.6016 -266865.8969 -222076.5868 161.8932 -4600.9410 -2563.6019 921491.4634 -2547.9501 -2620.2321
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 300
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 300
WRITING COORDINATES TO RESTART FILE AT STEP 300
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO DCD FILE AT STEP 300
WRITING VELOCITIES TO RESTART FILE AT STEP 300
FINISHED WRITING RESTART VELOCITIES
WRITING FORCES TO DCD FILE AT STEP 300
The last force output (seq=300) takes 0.001 seconds, 522.258 MB of memory in use
TIMING: 320 CPU: 715.789, 2.28438/step Wall: 715.789, 2.28438/step, 0.114219 hours remaining, 522.257812 MB of memory in use.
ENERGY: 320 21393.3837 20196.2689 5687.3971 178.9168 -337738.1163 22532.5474 0.0000 0.0000 45250.4880 -222499.1143 164.6088 -267749.6023 -222076.2070 162.2028 -3895.6023 -2553.5002 921491.4634 -2328.6776 -2419.9928
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 320
TIMING: 340 CPU: 759.661, 2.1936/step Wall: 759.661, 2.1936/step, 0.0974932 hours remaining, 522.257812 MB of memory in use.
ENERGY: 340 20898.6070 20139.5371 5681.9995 179.9655 -337821.3685 22621.7133 0.0000 0.0000 45758.5736 -222540.9726 166.4571 -268299.5461 -222070.3954 162.0722 -2966.9711 -2503.9486 921491.4634 -2588.8195 -2572.6687
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 340
WRITING VELOCITIES TO DCD FILE AT STEP 350
TIMING: 360 CPU: 803.507, 2.19228/step Wall: 803.507, 2.19228/step, 0.0852555 hours remaining, 522.257812 MB of memory in use.
ENERGY: 360 21112.5819 20418.0332 5690.9152 182.1442 -338077.5533 22797.1679 0.0000 0.0000 45362.4587 -222514.2522 165.0162 -267876.7109 -222065.3874 162.0273 -3505.9505 -2622.8573 921491.4634 -2490.4406 -2393.7696
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 360
TIMING: 380 CPU: 847.307, 2.19001/step Wall: 847.307, 2.19001/step, 0.0730002 hours remaining, 522.257812 MB of memory in use.
ENERGY: 380 21458.1131 20605.4124 5719.3306 183.8284 -338176.3491 22892.6556 0.0000 0.0000 44833.7911 -222483.2180 163.0930 -267317.0091 -222063.6479 162.7435 -4580.2695 -2564.2094 921491.4634 -2525.8342 -2510.8983
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 380
LDB: ============= START OF LOAD BALANCING ============== 887.953
LDB: ============== END OF LOAD BALANCING =============== 887.953
LDB: =============== DONE WITH MIGRATION ================ 887.954
Info: Benchmark time: 1 CPUs 2.20997 s/step 25.5783 days/ns 522.258 MB memory
TIMING: 400 CPU: 891.099, 2.18961/step Wall: 891.099, 2.18961/step, 0.0608225 hours remaining, 522.257812 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 400 21983.9558 19981.4885 5714.2278 174.7230 -338264.6770 23090.3582 0.0000 0.0000 44890.2665 -222429.6571 163.2985 -267319.9237 -222060.6832 162.8388 -4748.6063 -2656.9982 921491.4634 -2158.0490 -2271.9637
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 400
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 400
WRITING COORDINATES TO RESTART FILE AT STEP 400
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO DCD FILE AT STEP 400
WRITING VELOCITIES TO RESTART FILE AT STEP 400
FINISHED WRITING RESTART VELOCITIES
WRITING FORCES TO DCD FILE AT STEP 400
The last force output (seq=400) takes 0.001 seconds, 522.258 MB of memory in use
TIMING: 420 CPU: 934.917, 2.19089/step Wall: 934.917, 2.19089/step, 0.0486865 hours remaining, 522.257812 MB of memory in use.
ENERGY: 420 21812.8762 19887.3915 5695.0414 180.6770 -338321.5524 23183.0570 0.0000 0.0000 45121.9789 -222440.5303 164.1414 -267562.5093 -222061.1146 162.9616 -3051.6035 -2402.9277 921491.4634 -2326.3105 -2390.6551
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 420
TIMING: 440 CPU: 978.621, 2.1852/step Wall: 978.621, 2.1852/step, 0.0364201 hours remaining, 522.257812 MB of memory in use.
ENERGY: 440 22071.5689 20036.2374 5729.7526 186.7201 -338123.1813 23276.2503 0.0000 0.0000 44417.5445 -222405.1075 161.5788 -266822.6520 -222059.4769 163.3965 -2408.4610 -2197.9666 921491.4634 -2368.2456 -2261.8282
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 440
WRITING VELOCITIES TO DCD FILE AT STEP 450
TIMING: 460 CPU: 1022.31, 2.18469/step Wall: 1022.31, 2.18469/step, 0.0242744 hours remaining, 522.257812 MB of memory in use.
ENERGY: 460 21262.6143 19597.9054 5728.0971 179.4910 -338014.3782 23341.8018 0.0000 0.0000 45423.8573 -222480.6113 165.2395 -267904.4687 -222064.6833 163.1399 -3669.8199 -2365.2407 921491.4634 -2361.3463 -2290.1068
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 460
TIMING: 480 CPU: 1066.04, 2.18641/step Wall: 1066.04, 2.18641/step, 0.0121467 hours remaining, 522.257812 MB of memory in use.
ENERGY: 480 21624.0329 19623.1957 5725.3111 190.1901 -337854.6824 23181.5165 0.0000 0.0000 45051.6817 -222458.7544 163.8856 -267510.4361 -222064.6204 163.1550 -4077.7313 -2291.4877 921491.4634 -2217.8613 -2298.7163
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 480
Info: Benchmark time: 1 CPUs 2.18259 s/step 25.2615 days/ns 523.312 MB memory
TIMING: 500 CPU: 1109.36, 2.16577/step Wall: 1109.36, 2.16577/step, 0 hours remaining, 523.312500 MB of memory in use.
ENERGY: 500 20974.8940 19756.6574 5724.4523 179.8271 -337741.4201 23251.1012 0.0000 0.0000 45359.0795 -222495.4086 165.0039 -267854.4880 -222061.0904 163.5315 -3197.5165 -2425.4138 921491.4634 -2247.8852 -2323.0617
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500
WRITING COORDINATES TO DCD FILE apoa1-out.dcd AT STEP 500
WRITING COORDINATES TO RESTART FILE AT STEP 500
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO DCD FILE AT STEP 500
WRITING VELOCITIES TO RESTART FILE AT STEP 500
FINISHED WRITING RESTART VELOCITIES
WRITING FORCES TO DCD FILE AT STEP 500
The last force output (seq=500) takes 0.001 seconds, 523.312 MB of memory in use
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
WRITING COORDINATES TO OUTPUT FILE AT STEP 500
CLOSING COORDINATE DCD FILE apoa1-out.dcd
WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
CLOSING VELOCITY DCD FILE
CLOSING FORCE DCD FILE
====================================================
WallClock: 1110.744385 CPUTime: 1110.744385 Memory: 523.312500 MB
[Partition 0][Node 0] End of program
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 100 # Restart file frequency
DCDfreq 20 # Trajectory file frequency
velDCDfreq 50 # Trajectory file frequency
forceDCDfreq 100 # Trajectory file frequency
This source diff could not be displayed because it is too large. You can view the blob instead.
This source diff could not be displayed because it is too large. You can view the blob instead.
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
REMARKS AUTOMATICALLY CONVERTED FROM FILE charmm/par_all22_prot_lipid.inp
REMARKS FILENAME="par_all22_prot_lipid.xplor"
SET ECHO=FALSE END
{ >>>>>>>>>>>> Combined Parameter File for Proteins <<<<<<<<<<<<< }
{ >>>>>>>>>>>>>>>>>>>>>>>> and Lipids <<<<<<<<<<<<<<<<<<<<<<<<<<< }
{ >>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<< }
{ >>>>>>>>>>>>>>>>>>>>> January 1996 <<<<<<<<<<<<<<<<<<<<<<<<<<<< }
{ >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< }
{ >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< }
{ These files are a beta release; additional parameter development }
{ and testing may lead to alteration of the contents. }
BOND C C 600.000 1.3350 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
BOND CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
BOND CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
BOND CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
BOND CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
BOND CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
BOND CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
BOND CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND CPB C 450.000 1.3800 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
BOND CPB CPA 299.800 1.4432 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
BOND CPB CPB 340.700 1.3464 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
BOND CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
BOND CPM CPA 360.000 1.3716 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
BOND CPT CA 305.000 1.3680 ! ALLOW ARO
! adm jr., 12/30/91, for jwk
BOND CPT CPT 360.000 1.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
BOND CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
BOND CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
BOND CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
BOND CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
BOND CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
BOND CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
BOND CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
BOND CT2 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
BOND CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
BOND CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
BOND CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
BOND CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
BOND CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
BOND CT3 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
BOND CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
BOND CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
BOND CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND CY CA 350.000 1.3650 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
BOND CY CPT 350.000 1.4400 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
BOND CY CT2 230.000 1.5100 ! ALLOW ARO
!JWK Kb from alkane freq.. b0 from TRP crystal
BOND FE CM 258.000 1.9000 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
BOND FE CPM 0.000 3.3814 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
BOND H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
BOND HA C 330.000 1.1000 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
BOND HA CA 340.000 1.0830 ! ALLOW ARO
! trp, adm jr., 10/02/89
BOND HA CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
BOND HA CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND HA CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND HA CPM 367.600 1.0900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
BOND HA CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
BOND HA CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND HA CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
BOND HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
BOND HA1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
BOND HA2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
BOND HB CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
BOND HB CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
BOND HB CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
BOND HB CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
BOND HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89