|
|
|
``` |
|
# STEP Elec vdW dE dE_avg Temp dG |
|
# l l+dl l l+dl E(l+dl)-E(l) |
|
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.05 |
|
FepEnergy: 50 -173267.1741 -173265.5731 3721.3632 3721.3632 1.6010 -36368.9256 299.8270 -9999999999.9999 |
|
FepEnergy: 100 -172961.1502 -172958.8260 3480.1072 3480.1072 2.3242 -36363.8878 299.2973 -9999999999.9999 |
|
FepEnergy: 150 -173046.4077 -173044.0104 3545.0965 3545.0965 2.3973 -36364.7943 298.6183 -9999999999.9999 |
|
FepEnergy: 200 -173126.0777 -173123.8534 3507.0219 3507.0219 2.2243 -36357.7866 300.8991 -9999999999.9999 |
|
FepEnergy: 250 -173144.6532 -173142.3190 3543.7177 3543.7177 2.3342 -36349.6853 299.4086 -9999999999.9999 |
|
``` |
|
|
|
|
|
``` |
|
TACC: Starting up job 7023336 |
|
TACC: Setting up parallel environment for MVAPICH2+mpispawn. |
|
TACC: Starting parallel tasks... |
|
Charm++> Running on MPI version: 3.0 |
|
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE) |
|
Charm++> Running in non-SMP mode: numPes 256 |
|
Charm++> Using recursive bisection (scheme 3) for topology aware partitions |
|
Converse/Charm++ Commit ID: v6.7.1-rc1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Apr-16-49226 |
|
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'. |
|
CharmLB> Load balancer assumes all CPUs are same. |
|
Charm++> Running on 16 unique compute nodes (16-way SMP). |
|
Charm++> cpu topology info is gathered in 0.032 seconds. |
|
Info: NAMD 2.11 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 60701 for mpi-linux-x86_64 |
|
Info: Built Mon May 9 10:46:23 CDT 2016 by tg804216 on login2.stampede.tacc.utexas.edu |
|
Info: 1 NAMD 2.11 Linux-x86_64-MPI 256 c470-904.stampede.tacc.utexas.edu tg804216 |
|
Info: Running on 256 processors, 256 nodes, 16 physical nodes. |
|
Info: CPU topology information available. |
|
Info: Charm++/Converse parallel runtime startup completed at 0.122841 s |
|
Info: 273.676 MB of memory in use based on /proc/self/stat |
|
Info: Configuration file is FEP01.conf |
|
Info: Working in the current directory /scratch/01143/tg804216/proj8/SimsInputs/3D4S/fepK6 |
|
TCL: Suspending until startup complete. |
|
Info: EXTENDED SYSTEM FILE eq9.xsc |
|
Info: SIMULATION PARAMETERS: |
|
Info: TIMESTEP 2 |
|
Info: NUMBER OF STEPS 0 |
|
Info: STEPS PER CYCLE 20 |
|
Info: PERIODIC CELL BASIS 1 81.2352 0 0 |
|
Info: PERIODIC CELL BASIS 2 0 80.2855 0 |
|
Info: PERIODIC CELL BASIS 3 0 0 101.861 |
|
Info: PERIODIC CELL CENTER 0 0 0 |
|
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. |
|
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: REMOVING LOAD FROM NODE 0 |
|
Info: REMOVING PATCHES FROM PROCESSOR 0 |
|
Info: MIN ATOMS PER PATCH 40 |
|
Info: VELOCITY FILE eq9.vel |
|
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 fep01.dcd |
|
Info: DCD FREQUENCY 2500 |
|
Info: DCD FIRST STEP 2500 |
|
Info: DCD FILE WILL CONTAIN UNIT CELL DATA |
|
Info: XST FILENAME fep01.xst |
|
Info: XST FREQUENCY 2500 |
|
Info: NO VELOCITY DCD OUTPUT |
|
Info: NO FORCE DCD OUTPUT |
|
Info: OUTPUT FILENAME fep01 |
|
Info: BINARY OUTPUT FILES WILL BE USED |
|
Info: RESTART FILENAME fep01.restart |
|
Info: RESTART FREQUENCY 2500 |
|
Info: BINARY RESTART FILES WILL BE USED |
|
Info: SWITCHING ACTIVE |
|
Info: VDW FORCE 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 1.008 |
|
Info: HYDROGEN GROUP CUTOFF 2.8 |
|
Info: PATCH DIMENSION 17.808 |
|
Info: ENERGY OUTPUT STEPS 2500 |
|
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL |
|
Info: TIMING OUTPUT STEPS 2500 |
|
Info: ALCHEMICAL FEP ON |
|
Info: FEP CURRENT LAMBDA VALUE 0 |
|
Info: FEP COMPARISON LAMBDA VALUE 0.05 |
|
Info: FEP INTRA-ALCHEMICAL NON-BONDED INTERACTIONS WILL BE RETAINED |
|
Info: FEP INTRA-ALCHEMICAL BONDED INTERACTIONS WILL BE RETAINED |
|
Info: FEP VDW SHIFTING COEFFICIENT 6 |
|
Info: FEP ELEC. ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5 |
|
Info: FEP ELEC. ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1 |
|
Info: FEP VDW ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND LAMBDA = 1 |
|
Info: FEP VDW ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 0.5 |
|
Info: FEP BOND ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1 |
|
Info: FEP BOND ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND LAMBDA = 1 |
|
Info: COLLECTIVE VARIABLES CALCULATION REQUESTED |
|
Info: COLLECTIVE VARIABLES CONFIGURATION rest.in |
|
Info: LANGEVIN DYNAMICS ACTIVE |
|
Info: LANGEVIN TEMPERATURE 300 |
|
Info: LANGEVIN USING BBK INTEGRATOR |
|
Info: LANGEVIN DAMPING COEFFICIENT IS 0.1 INVERSE PS |
|
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS |
|
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE |
|
Info: TARGET PRESSURE IS 1 BAR |
|
Info: OSCILLATION PERIOD IS 200 FS |
|
Info: DECAY TIME IS 100 FS |
|
Info: PISTON TEMPERATURE IS 300 K |
|
Info: PRESSURE CONTROL IS GROUP-BASED |
|
Info: INITIAL STRAIN RATE IS 2.03684e-05 2.03684e-05 -4.36381e-07 |
|
Info: CELL FLUCTUATION IS ANISOTROPIC |
|
Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE |
|
Info: PARTICLE MESH EWALD (PME) ACTIVE |
|
Info: PME TOLERANCE 1e-06 |
|
Info: PME EWALD COEFFICIENT 0.257952 |
|
Info: PME INTERPOLATION ORDER 6 |
|
Info: PME GRID DIMENSIONS 84 84 108 |
|
Info: PME MAXIMUM GRID SPACING 1 |
|
Info: Attempting to read FFTW data from FFTW_NAMD_2.11_Linux-x86_64-MPI.txt |
|
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. |
|
Info: Writing FFTW data to FFTW_NAMD_2.11_Linux-x86_64-MPI.txt |
|
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2 |
|
Info: USING VERLET I (r-RESPA) MTS SCHEME. |
|
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS |
|
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS |
|
Info: RIGID BONDS TO HYDROGEN : ALL |
|
Info: ERROR TOLERANCE : 1e-08 |
|
Info: MAX ITERATIONS : 100 |
|
Info: RIGID WATER USING SETTLE ALGORITHM |
|
Info: RANDOM NUMBER SEED 1462873598 |
|
Info: USE HYDROGEN BONDS? NO |
|
Info: COORDINATE PDB ../out7_ions.pdb |
|
Info: STRUCTURE FILE ../out7_ions.psf |
|
Info: PARAMETER file: CHARMM format! |
|
Info: PARAMETERS ../../toppar/par_all36_prot.prm |
|
Info: PARAMETERS ../../toppar/par_all36_na.prm |
|
Info: PARAMETERS ../../toppar/par_all36_carb.prm |
|
Info: PARAMETERS ../../toppar/par_all36_lipid.prm |
|
Info: PARAMETERS ../../toppar/par_all36_cgenff.prm |
|
Info: PARAMETERS ../../toppar/chol.prm |
|
Info: PARAMETERS ../../toppar/wation.prm |
|
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS |
|
Info: BINARY COORDINATES eq9.coor |
|
Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT |
|
Info: SUMMARY OF PARAMETERS: |
|
Info: 939 BONDS |
|
Info: 2773 ANGLES |
|
Info: 6799 DIHEDRAL |
|
Info: 193 IMPROPER |
|
Info: 6 CROSSTERM |
|
Info: 350 VDW |
|
Info: 23 VDW_PAIRS |
|
Info: 0 NBTHOLE_PAIRS |
|
Warning: Residue 20 out of order in segment O1, lookup for additional residues in this segment disabled. |
|
Info: TIME FOR READING PSF FILE: 7.88427 |
|
Info: Reading pdb file ../out7_ions.pdb |
|
Info: TIME FOR READING PDB FILE: 0.124348 |
|
Info: |
|
Info: To read alchdata from file: ../out9_alchfile.pdb |
|
Info: To read alchflag data from column: 5 |
|
Info: **************************** |
|
Info: STRUCTURE SUMMARY: |
|
Info: 69634 ATOMS |
|
Info: 56966 BONDS |
|
Info: 73525 ANGLES |
|
Info: 88042 DIHEDRALS |
|
Info: 1032 IMPROPERS |
|
Info: 275 CROSSTERMS |
|
Info: 0 EXCLUSIONS |
|
Info: 56919 RIGID BONDS |
|
Info: ALCH: 74 ATOMS TO DISAPPEAR IN FINAL STATE |
|
Info: ALCH: 0 ATOMS TO APPEAR IN FINAL STATE |
|
Info: 151983 DEGREES OF FREEDOM |
|
Info: 25417 HYDROGEN GROUPS |
|
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP |
|
Info: 25417 MIGRATION GROUPS |
|
Info: 4 ATOMS IN LARGEST MIGRATION GROUP |
|
Info: TOTAL MASS = 413314 amu |
|
Info: TOTAL CHARGE = 9.818e-06 e |
|
Info: MASS DENSITY = 1.03312 g/cm^3 |
|
Info: ATOM DENSITY = 0.104817 atoms/A^3 |
|
Info: ***************************** |
|
Info: Reading from binary file eq9.coor |
|
Info: |
|
Info: Entering startup at 29.7645 s, 399.152 MB of memory in use |
|
Info: Startup phase 0 took 0.00476599 s, 399.152 MB of memory in use |
|
Info: ADDED 217340 IMPLICIT EXCLUSIONS |
|
Info: Startup phase 1 took 0.125727 s, 410.609 MB of memory in use |
|
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 |
|
Info: NONBONDED TABLE SIZE: 769 POINTS |
|
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556 |
|
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556 |
|
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.6778e-33 AT 11.9974 |
|
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 3.71539e-17 AT 11.9974 |
|
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 |
|
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 9.34011e-27 AT 11.9974 |
|
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.98256e-17 AT 11.9974 |
|
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 |
|
Info: Startup phase 2 took 0.0123639 s, 414.352 MB of memory in use |
|
Info: Startup phase 3 took 0.000324965 s, 414.352 MB of memory in use |
|
Info: Startup phase 4 took 0.00302601 s, 414.352 MB of memory in use |
|
Info: Startup phase 5 took 0.000293016 s, 414.352 MB of memory in use |
|
Info: PATCH GRID IS 9 (PERIODIC) BY 4 (PERIODIC) BY 5 (PERIODIC) |
|
Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY |
|
Info: Reading from binary file eq9.vel |
|
Info: REMOVING COM VELOCITY 0.00634616 0.00950085 -0.00831659 |
|
Info: LARGEST PATCH (136) HAS 435 ATOMS |
|
Info: TORUS A SIZE 256 USING 0 16 32 48 64 80 96 112 128 144 160 176 192 208 224 240 |
|
Info: TORUS B SIZE 1 USING 0 |
|
Info: TORUS C SIZE 1 USING 0 |
|
Info: TORUS MINIMAL MESH SIZE IS 241 BY 1 BY 1 |
|
Info: Placed 100% of base nodes on same physical node as patch |
|
Info: Startup phase 6 took 0.061497 s, 430.035 MB of memory in use |
|
Info: PME using 42 and 42 processors for FFT and reciprocal sum. |
|
Info: PME GRID LOCATIONS: 7 15 23 27 31 39 47 55 59 63 ... |
|
Info: PME TRANS LOCATIONS: 3 11 13 19 29 35 43 45 51 53 ... |
|
Info: PME USING 42 GRID NODES AND 42 TRANS NODES |
|
Info: Startup phase 7 took 0.0121171 s, 430.035 MB of memory in use |
|
Info: Startup phase 8 took 0.076756 s, 435.191 MB of memory in use |
|
LDB: Central LB being created... |
|
Info: Startup phase 9 took 0.0531468 s, 435.191 MB of memory in use |
|
Info: CREATING 6300 COMPUTE OBJECTS |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Initializing the collective variables module, version 2016-05-03. |
|
colvars: Please cite Fiorin et al, Mol Phys 2013 in any publication based on this calculation. |
|
colvars: Using NAMD interface, version 2016-04-28. |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Reading new configuration from file "rest.in": |
|
colvars: # indexFile = "" [default] |
|
colvars: # analysis = off [default] |
|
colvars: # colvarsTrajFrequency = 500 |
|
colvars: # colvarsRestartFrequency = 500 |
|
colvars: # colvarsTrajAppend = off [default] |
|
colvars: # scriptedColvarForces = off [default] |
|
colvars: # scriptingAfterBiases = on [default] |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Initializing a new collective variable. |
|
colvars: # name = rmsd_rest_402 |
|
colvars: Initializing a new "rmsd" component. |
|
colvars: # componentCoeff = 1 [default] |
|
colvars: # componentExp = 1 [default] |
|
colvars: # period = 0 [default] |
|
colvars: # wrapAround = 0 [default] |
|
colvars: # scalable = on [default] |
|
colvars: Scalable calculation is not available for group "atoms" with the current configuration. |
|
colvars: Initializing atom group "atoms". |
|
colvars: # indexGroup = "" [default] |
|
colvars: # psfSegID = [default] |
|
colvars: # atomsFile = "" [default] |
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] |
|
colvars: # enableForces = on [default] |
|
colvars: # centerReference = on |
|
colvars: # rotateReference = on |
|
colvars: # enableFitGradients = on [default] |
|
colvars: Within atom group "atoms": |
|
colvars: Defining atom group "refPositionsGroup". |
|
colvars: Initializing atom group "refPositionsGroup". |
|
colvars: # indexGroup = "" [default] |
|
colvars: # psfSegID = [default] |
|
colvars: # atomsFile = rest_ref.pdb |
|
colvars: # atomsCol = O |
|
colvars: # atomsColValue = 0 [default] |
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] |
|
colvars: # enableForces = on [default] |
|
colvars: # centerReference = off [default] |
|
colvars: # rotateReference = off [default] |
|
colvars: # enableFitGradients = on [default] |
|
colvars: Atom group "refPositionsGroup" defined, 88 atoms initialized: total mass = 1056.97, total charge = 5.84. |
|
colvars: # refPositions = [default] |
|
colvars: # refPositionsFile = rest_ref.pdb |
|
colvars: # refPositionsCol = "" [default] |
|
colvars: Warning: atom group "atoms" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use refPositionsGroup (or a different definition for it if already defined) to align the coordinates. |
|
colvars: Atom group "atoms" defined, 11 atoms initialized: total mass = 132.121, total charge = -1.23. |
|
colvars: The option "refPositionsGroup" (alternative group for fitting) was enabled: Jacobian derivatives of the RMSD will not be calculated. |
|
colvars: # refPositions = [default] |
|
colvars: # refPositionsFile = rest_ref.pdb |
|
colvars: # refPositionsCol = "" [default] |
|
colvars: WARNING: explicit fitting parameters were provided for atom group "atoms". |
|
colvars: All components initialized. |
|
colvars: # width = 1 |
|
colvars: # lowerBoundary = 0 |
|
colvars: # lowerWallConstant = 0 |
|
colvars: # upperBoundary = 0.7 |
|
colvars: # upperWallConstant = 100 |
|
colvars: # upperWall = 0.7 [default] |
|
colvars: # hardLowerBoundary = off [default] |
|
colvars: # hardUpperBoundary = off [default] |
|
colvars: # expandBoundaries = off [default] |
|
colvars: # extendedLagrangian = off [default] |
|
colvars: # outputValue = on [default] |
|
colvars: # outputVelocity = off [default] |
|
colvars: # outputSystemForce = off [default] |
|
colvars: # outputAppliedForce = off [default] |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Initializing a new collective variable. |
|
colvars: # name = chol_dist |
|
colvars: Initializing a new "distance" component. |
|
colvars: # componentCoeff = 1 [default] |
|
colvars: # componentExp = 1 [default] |
|
colvars: # period = 0 [default] |
|
colvars: # wrapAround = 0 [default] |
|
colvars: # scalable = on [default] |
|
colvars: # forceNoPBC = off [default] |
|
colvars: # oneSiteSystemForce = off [default] |
|
colvars: Will enable scalable calculation for group "group1". |
|
colvars: Initializing atom group "group1". |
|
colvars: # indexGroup = "" [default] |
|
colvars: # psfSegID = [default] |
|
colvars: # atomsFile = "" [default] |
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] |
|
colvars: # enableForces = on [default] |
|
colvars: # centerReference = on |
|
colvars: # rotateReference = on |
|
colvars: # enableFitGradients = on [default] |
|
colvars: Within atom group "group1": |
|
colvars: Defining atom group "refPositionsGroup". |
|
colvars: Initializing atom group "refPositionsGroup". |
|
colvars: # indexGroup = "" [default] |
|
colvars: # psfSegID = [default] |
|
colvars: # atomsFile = rest_ref.pdb |
|
colvars: # atomsCol = O |
|
colvars: # atomsColValue = 0 [default] |
|
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] |
|
colvars: # enableForces = on [default] |
|
colvars: # centerReference = off [default] |
|
colvars: # rotateReference = off [default] |
|
colvars: # enableFitGradients = on [default] |
|
colvars: Atom group "refPositionsGroup" defined, 88 atoms initialized: total mass = 1056.97, total charge = 5.84. |
|
colvars: # refPositions = [default] |
|
colvars: # refPositionsFile = rest_ref.pdb |
|
colvars: # refPositionsCol = "" [default] |
|
colvars: Warning: atom group "group1" will be aligned to a fixed orientation given by the reference positions provided. If the internal structure of the group changes too much (i.e. its RMSD is comparable to its radius of gyration), the optimal rotation and its gradients may become discontinuous. If that happens, use refPositionsGroup (or a different definition for it if already defined) to align the coordinates. |
|
colvars: Atom group "group1" defined, 11 atoms initialized: total mass = 132.121, total charge = -1.23. |
|
colvars: Will enable scalable calculation for group "group2". |
|
colvars: Initializing atom group "group2". |
|
colvars: # indexGroup = "" [default] |
|
colvars: # psfSegID = [default] |
|
colvars: # atomsFile = "" [default] |
|
colvars: # dummyAtom = ( 0.827 , 0.65 , -2.623 ) |
|
colvars: # centerReference = off [default] |
|
colvars: # rotateReference = off [default] |
|
colvars: # enableFitGradients = on [default] |
|
colvars: Atom group "group2" defined, 0 atoms initialized: total mass = 1, total charge = 0. |
|
colvars: All components initialized. |
|
colvars: # width = 1 |
|
colvars: # lowerBoundary = 0 |
|
colvars: # lowerWallConstant = 0 |
|
colvars: # upperBoundary = 3 |
|
colvars: # upperWallConstant = 100 |
|
colvars: # upperWall = 3 [default] |
|
colvars: # hardLowerBoundary = off [default] |
|
colvars: # hardUpperBoundary = off [default] |
|
colvars: # expandBoundaries = off [default] |
|
colvars: # extendedLagrangian = off [default] |
|
colvars: # outputValue = on [default] |
|
colvars: # outputVelocity = off [default] |
|
colvars: # outputSystemForce = off [default] |
|
colvars: # outputAppliedForce = off [default] |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Collective variables initialized, 2 in total. |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Initializing a new "harmonic" instance. |
|
colvars: # name = "harmonic1" [default] |
|
colvars: # colvars = { rmsd_rest_402 } |
|
colvars: # outputEnergy = off [default] |
|
colvars: # forceConstant = 0 |
|
colvars: # centers = { 0 } |
|
colvars: # targetCenters = { 0 } [default] |
|
colvars: # targetForceConstant = 0 [default] |
|
colvars: # outputCenters = off [default] |
|
colvars: ---------------------------------------------------------------------- |
|
colvars: Initializing a new "harmonic" instance. |
|
colvars: # name = "harmonic2" [default] |
|
colvars: # colvars = { chol_dist } |
|
colvars: # outputEnergy = off [default] |
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colvars: # forceConstant = 0 |
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colvars: # centers = { 0 } |
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colvars: # targetCenters = { 0 } [default] |
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colvars: # targetForceConstant = 0 [default] |
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colvars: # outputCenters = off [default] |
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colvars: ---------------------------------------------------------------------- |
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colvars: Collective variables biases initialized, 2 in total. |
|
colvars: ---------------------------------------------------------------------- |
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colvars: Collective variables module (re)initialized. |
|
colvars: ---------------------------------------------------------------------- |
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colvars: Updating NAMD interface: |
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colvars: updating atomic data (99 atoms). |
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colvars: updating group data (1 scalable groups, 11 atoms in total). |
|
colvars: Re-initialized atom group rmsd_rest_402:0/0. 11 atoms: total mass = 132.121. |
|
colvars: Re-initialized atom group chol_dist:0/0. 11 atoms: total mass = 132.121. |
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colvars: Re-initialized atom group chol_dist:0/1. 0 atoms: total mass = 1. |
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colvars: The restart output state file will be "fep01.restart.colvars.state". |
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colvars: The final output state file will be "fep01.colvars.state". |
|
colvars: Writing to colvar trajectory file "fep01.colvars.traj". |
|
Info: Startup phase 10 took 0.543938 s, 435.191 MB of memory in use |
|
Info: useSync: 1 useProxySync: 0 |
|
Info: Startup phase 11 took 0.000968933 s, 435.191 MB of memory in use |
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Info: Startup phase 12 took 0.000125885 s, 435.191 MB of memory in use |
|
Info: Finished startup at 30.6595 s, 435.191 MB of memory in use |
|
|
|
TCL: Running for 1000000 steps |
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colvars: Updating NAMD interface: |
|
colvars: updating atomic data (99 atoms). |
|
colvars: updating group data (1 scalable groups, 11 atoms in total). |
|
FEP: RESETTING FOR NEW FEP WINDOW LAMBDA SET TO 0 LAMBDA2 0.05 |
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FEP: WINDOW TO HAVE 300000 STEPS OF EQUILIBRATION PRIOR TO FEP DATA COLLECTION. |
|
FEP: USING CONSTANT TEMPERATURE OF 300 K FOR FEP CALCULATION |
|
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG |
|
|
|
ENERGY: 0 3890.8379 19121.1035 12892.7708 231.7270 -173040.0542 3646.2544 0.0000 0.0000 45249.3689 -88007.9917 299.6456 -133257.3606 -87684.2150 299.6456 94.2039 118.9193 664336.2988 94.2039 118.9193 |
|
|
|
OPENING FEP ENERGY OUTPUT FILE |
|
OPENING EXTENDED SYSTEM TRAJECTORY FILE |
|
LDB: ============= START OF LOAD BALANCING ============== 31.0167 |
|
LDB: ============== END OF LOAD BALANCING =============== 31.039 |
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Info: useSync: 1 useProxySync: 0 |
|
LDB: =============== DONE WITH MIGRATION ================ 31.0398 |
|
LDB: ============= START OF LOAD BALANCING ============== 31.9022 |
|
LDB: Largest compute 2586 load 0.120326 is 30.1% of average load 0.399465 |
|
LDB: Average compute 0.012671 is 3.2% of average load 0.399465 |
|
LDB: Partitioning computes with target load 0.039947 |
|
LDB: Increased migratable compute count from 5040 to 5680 |
|
LDB: Largest unpartitionable compute is 0.018083 |
|
``` |
Test using TI (alchType TI) and same seed as simulation above with FEP
ti.out
logfile