Info: NAMD 2.6 for Linux-amd64 Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@ks.uiuc.edu 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 50900 for net-linux-amd64-iccstatic Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu Info: 1 NAMD 2.6 Linux-amd64 1 tashkent.ks.uiuc.edu jcomer Info: Running on 1 processors. Info: 7604 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is eq2.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE eq1.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 500 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 34.1775 19.7324 0 Info: PERIODIC CELL BASIS 2 0 39.4648 0 Info: PERIODIC CELL BASIS 3 0 0 17.412 Info: PERIODIC CELL CENTER 0 0 0 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER. Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: MAX SELF PARTITIONS 50 Info: MAX PAIR PARTITIONS 20 Info: SELF PARTITION ATOMS 125 Info: PAIR PARTITION ATOMS 200 Info: PAIR2 PARTITION ATOMS 400 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE eq1.vel Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME eq2.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME eq2.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME eq2 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME eq2.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 14 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 3 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 100 Info: HARMONIC CONSTRAINTS ACTIVE Info: HARMONIC CONS EXP 2 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS 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 48 48 128 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-amd64.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-amd64.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: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1175903466 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../1_build/membrane_hex.pdb Info: STRUCTURE FILE ../1_build/membrane_hex.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_silicon_ions_NEW0.1.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES eq1.coor Info: SUMMARY OF PARAMETERS: Info: 11 BONDS Info: 36 ANGLES Info: 0 DIHEDRAL Info: 0 IMPROPER Info: 0 CROSSTERM Info: 15 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 2268 ATOMS Info: 3888 BONDS Info: 9720 ANGLES Info: 0 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 2268 CONSTRAINTS Info: 6804 DEGREES OF FREEDOM Info: 2268 HYDROGEN GROUPS Info: TOTAL MASS = 45452.2 amu Info: TOTAL CHARGE = 3.86238e-05 e Info: ***************************** Info: Entering startup phase 0 with 8776 kB of memory in use. Info: Entering startup phase 1 with 8776 kB of memory in use. Info: Entering startup phase 2 with 8776 kB of memory in use. Info: Entering startup phase 3 with 8776 kB of memory in use. Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 1 (PERIODIC) Info: REMOVING COM VELOCITY -0.101547 -0.00719337 0.0538238 Info: LARGEST PATCH (0) HAS 2268 ATOMS Info: CREATING 322 COMPUTE OBJECTS Info: Entering startup phase 4 with 8776 kB 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: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Entering startup phase 5 with 10264 kB of memory in use. Info: Entering startup phase 6 with 10264 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 10264 kB of memory in use. Info: CREATING 322 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Entering startup phase 8 with 10452 kB of memory in use. Info: Finished startup with 10708 kB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 5.6090 0.1027 0.0000 0.0000 -306965.1214 -2069.1787 37.0337 0.0000 2014.7648 -306976.7900 298.0234 -306975.2838 -306975.2838 298.0234 -123903.3956 -123903.3956 23485.4484 -123903.3956 -123903.3956 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 1 CPUs 0.12051 s/step 1.3948 days/ns 23952 kB memory TIMING: 100 CPU: 13.263, 0.120142/step Wall: 13.5632, 0.122153/step, 0.0135726 hours remaining, 23952 kB of memory in use. ENERGY: 100 41.0360 0.7490 0.0000 0.0000 -308168.3739 -1707.9030 443.7702 0.0000 2182.6456 -307208.0761 322.8563 -307206.6417 -307205.3973 336.1542 -118367.3506 -118367.3506 23485.4484 -123416.5770 -123416.5770 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 100 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 100 WRITING COORDINATES TO RESTART FILE AT STEP 100 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 100 FINISHED WRITING RESTART VELOCITIES Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Info: Initial time: 1 CPUs 0.117876 s/step 1.36431 days/ns 24524 kB memory TIMING: 200 CPU: 24.8702, 0.116072/step Wall: 25.5157, 0.119525/step, 0.00996039 hours remaining, 24524 kB of memory in use. ENERGY: 200 44.3319 0.7885 0.0000 0.0000 -307940.6135 -2204.7428 377.7372 0.0000 2322.6383 -307399.8604 343.5640 -307398.7042 -307395.4330 334.4673 -124027.7151 -124027.7151 23485.4484 -121295.9841 -121295.9841 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 200 WRITING COORDINATES TO DCD FILE AT STEP 200 WRITING COORDINATES TO RESTART FILE AT STEP 200 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 200 FINISHED WRITING RESTART VELOCITIES Warning: Not all atoms have unique coordinates. Warning: Not all atoms have unique coordinates. Info: Initial time: 1 CPUs 0.118602 s/step 1.37271 days/ns 24532 kB memory TIMING: 300 CPU: 36.4845, 0.116142/step Wall: 37.5403, 0.120246/step, 0.00668033 hours remaining, 24532 kB of memory in use. ENERGY: 300 43.5597 0.7627 0.0000 0.0000 -308009.2428 -2272.0414 383.7776 0.0000 2215.5129 -307637.6712 327.7181 -307636.5056 -307633.1087 321.8864 -125984.9326 -125984.9326 23485.4484 -125295.7302 -125295.7302 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 300 WRITING COORDINATES TO DCD FILE AT STEP 300 WRITING COORDINATES TO RESTART FILE AT STEP 300 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 300 FINISHED WRITING RESTART VELOCITIES Info: Benchmark time: 1 CPUs 0.126085 s/step 1.45931 days/ns 24532 kB memory TIMING: 400 CPU: 48.4476, 0.119632/step Wall: 50.2948, 0.127546/step, 0.00354293 hours remaining, 24532 kB of memory in use. ENERGY: 400 45.5001 0.8192 0.0000 0.0000 -308050.5243 -2217.1503 425.2842 0.0000 2133.4116 -307662.6595 315.5737 -307661.3447 -307660.7288 311.8141 -124789.7949 -124789.7949 23485.4484 -124203.8065 -124203.8065 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 400 WRITING COORDINATES TO DCD FILE AT STEP 400 WRITING COORDINATES TO RESTART FILE AT STEP 400 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 400 FINISHED WRITING RESTART VELOCITIES Info: Benchmark time: 1 CPUs 0.122041 s/step 1.41251 days/ns 24560 kB memory TIMING: 500 CPU: 60.3388, 0.118912/step Wall: 62.4991, 0.122042/step, 0 hours remaining, 24560 kB of memory in use. ENERGY: 500 47.1228 0.8379 0.0000 0.0000 -308186.0809 -2123.9522 410.2212 0.0000 2032.8688 -307818.9824 300.7014 -307816.7149 -307818.4731 307.2439 -123921.2056 -123921.2056 23485.4484 -124598.0968 -124598.0968 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500 WRITING COORDINATES TO DCD FILE AT STEP 500 WRITING COORDINATES TO RESTART FILE AT STEP 500 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 500 FINISHED WRITING RESTART VELOCITIES WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500 CLOSING EXTENDED SYSTEM TRAJECTORY FILE WRITING COORDINATES TO OUTPUT FILE AT STEP 500 CLOSING COORDINATE DCD FILE WRITING VELOCITIES TO OUTPUT FILE AT STEP 500 ========================================== WallClock: 63.514774 CPUTime: 60.592789 Memory: 24560 kB