Re: mininization do not go on

From: muniyamuthu.raviprasad_at_ndsu.edu
Date: Mon May 10 2010 - 22:18:19 CDT

Hi

It seems you are using Langivin Dynamics with minimization

1] Minimization nothing to do with Langivin dynamics
2] Remove Langivin dynamics and run the simulation for minimization only

Ravi

> Hi,
> I am a begginer in using NAMD. I need some help.
> Im was running a process with 1000 steps of minimization.
> Misteriously at step number 594, the minimization do not go on.
> The program do not stoped and the process was still running for close 48
> hours beyound this step.
>
> I kill the process and start it again.
> The same problem happen again at the same step.
>
> Any idea???
>
> Here I paste part of the log file:
>
> Charm++: standalone mode (not using charmrun)
> Charm++> cpu topology info is being gathered.
> Charm++> Running on 1 unique compute nodes (2-way SMP).
> Info: NAMD 2.7b2 for Linux-x86
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_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 60103 for net-linux-iccstatic
> Info: Built Thu Nov 12 22:11:41 CST 2009 by jim on kyoto.ks.uiuc.edu
> Info: 1 NAMD 2.7b2 Linux-x86 1 hercules root
> Info: Running on 1 processors.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 497.387 s
> Info: 1.22373 MB of memory in use based on CmiMemoryUsage
> Info: Configuration file is hbs_wb_eq.conf
> TCL: Suspending until startup complete.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 2
> Info: NUMBER OF STEPS 0
> Info: STEPS PER CYCLE 2
> Info: PERIODIC CELL BASIS 1 75 0 0
> Info: PERIODIC CELL BASIS 2 0 75 0
> Info: PERIODIC CELL BASIS 3 0 0 75
> Info: PERIODIC CELL CENTER -2.09006 0.941683 0.231198
> Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
> Info: LDB PERIOD 400 steps
> Info: FIRST LDB TIMESTEP 10
> Info: LAST LDB TIMESTEP -1
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: PME BACKGROUND SCALING 1
> Info: MAX SELF PARTITIONS 20
> Info: MAX PAIR PARTITIONS 8
> Info: SELF PARTITION ATOMS 154
> Info: SELF2 PARTITION ATOMS 154
> Info: PAIR PARTITION ATOMS 318
> Info: PAIR2 PARTITION ATOMS 637
> Info: MIN ATOMS PER PATCH 100
> Info: INITIAL TEMPERATURE 310
> Info: CENTER OF MASS MOVING INITIALLY? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 1
> Info: DCD FILENAME HbS_wb_eq.dcd
> Info: DCD FREQUENCY 250
> Info: DCD FIRST STEP 250
> Info: DCD FILE WILL CONTAIN UNIT CELL DATA
> Info: XST FILENAME HbS_wb_eq.xst
> Info: XST FREQUENCY 250
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME HbS_wb_eq
> Info: RESTART FILENAME HbS_wb_eq.restart
> Info: RESTART FREQUENCY 500
> 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 0.48
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 16.48
> Info: ENERGY OUTPUT STEPS 100
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS 1000
> Info: PRESSURE OUTPUT STEPS 100
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 310
> Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
> Info: TARGET PRESSURE IS 1.01325 BAR
> Info: OSCILLATION PERIOD IS 100 FS
> Info: DECAY TIME IS 50 FS
> Info: PISTON TEMPERATURE IS 310 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Info: CELL FLUCTUATION IS ISOTROPIC
> 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 80 80 80
> Info: PME MAXIMUM GRID SPACING 1.5
> Info: Attempting to read FFTW data from FFTW_NAMD_2.7b2_Linux-x86.txt
> Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
> Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-x86.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 1273251414
> Info: USE HYDROGEN BONDS? NO
> Info: COORDINATE PDB solvate.pdb
> Info: STRUCTURE FILE solvate.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS par_all27_prot_lipid_na.inp
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
>
> Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
> PREVIOUS VALUES k=130 theta0=107.5 k_ub=0 r_ub=0
> USING VALUES k=130 theta0=107 k_ub=0 r_ub=0
> Info: SUMMARY OF PARAMETERS:
> Info: 299 BONDS
> Info: 729 ANGLES
> Info: 1145 DIHEDRAL
> Info: 84 IMPROPER
> Info: 0 CROSSTERM
> Info: 161 VDW
> Info: 0 VDW_PAIRS
> Info: TIME FOR READING PSF FILE: 7.12897
> Info: TIME FOR READING PDB FILE: 2.56296
> Info:
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 265092 ATOMS
> Info: 179892 BONDS
> Info: 102036 ANGLES
> Info: 24488 DIHEDRALS
> Info: 1772 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 0 EXCLUSIONS
> Info: 260540 RIGID BONDS
> Info: 534736 DEGREES OF FREEDOM
> Info: 89896 HYDROGEN GROUPS
> Info: TOTAL MASS = 1.6019e+06 amu
> Info: TOTAL CHARGE = -3.99999 e
> Info: MASS DENSITY = 6.30536 g/cm^3
> Info: ATOM DENSITY = 0.628366 atoms/A^3
> Info: *****************************
> Info:
> Info: Entering startup at 552.166 s, 50.1557 MB of memory in use
> Info: Startup phase 0 took 0.000130042 s, 50.1557 MB of memory in use
> Info: Startup phase 1 took 0.641273 s, 74.913 MB of memory in use
> Info: Startup phase 2 took 0.00824161 s, 76.9392 MB of memory in use
> Info: PATCH GRID IS 4 (PERIODIC) BY 4 (PERIODIC) BY 4 (PERIODIC)
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0.00731082 -0.0112501 0.00151134
> Info: LARGEST PATCH (0) HAS 5307 ATOMS
> Info: CREATING 8262 COMPUTE OBJECTS
> Info: Startup phase 3 took 0.885683 s, 106.874 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: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
> Info: Startup phase 4 took 0.0123439 s, 108.884 MB of memory in use
> Info: Startup phase 5 took 0.000182625 s, 108.884 MB of memory in use
> LDB: Measuring processor speeds ... Done.
> Info: Startup phase 6 took 0.00128818 s, 108.885 MB of memory in use
> Info: CREATING 8262 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 769 POINTS
> Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.3715e-16 AT 0.03125
> Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.00929e-16 AT 0.231756
> Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.70577e-22 AT 11.9974
> Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.80873e-16 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 2.38228e-22 AT 11.9974
> Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 5.04001e-17 AT 11.9974
> Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 2.77933e-22 AT 11.9974
> Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.45399e-16 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295
> Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974
> Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974
> Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138
> Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
> Info: Startup phase 7 took 0.0581199 s, 115.959 MB of memory in use
> Info: Startup phase 8 took 0.00137016 s, 124.094 MB of memory in use
> Info: Finished startup at 553.774 s, 124.094 MB of memory in use
>
> TCL: Minimizing for 1000 steps
> PRESSURE: 0 3.62146e+15 -1.62399e+14 -2.26077e+14 -1.62399e+14 3.4613e+15
> -7.97545e+13 -2.26077e+14 -7.97545e+13 3.84302e+15
> GPRESSURE: 0 3.62146e+15 -1.62399e+14 -2.26077e+14 -1.62399e+14 3.4613e+15
> -7.97545e+13 -2.26077e+14 -7.97545e+13 3.84302e+15
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 0 80216.1008 23405.4899 2361.1222
> 654.5612 -906979.3104 9999999999.9999 0.0000 0.0000
> 0.0000 9999999999.9999 0.0000 9999999999.9999
> 9999999999.9999 0.0000 9999999999.9999 9999999999.9999
> 421875.0000 9999999999.9999 9999999999.9999
>
>
> 593 steps ahead...
>
>
> PRESSURE: 594 1.06718e+09 1.42446e+06 766860 1.42446e+06 1.06901e+09
> 1.81625e+06 766860 1.81625e+06 1.06801e+09
> GPRESSURE: 594 1.08244e+09 1.00718e+06 1.4095e+06 561421 1.08537e+09
> 1.88606e+06 528432 1.58441e+06 1.08312e+09
> ENERGY: 594 7662422.3680 838588.0426 8095.7241
> 15721.8603 -298815.5319 1613292986.3079 0.0000
> 0.0000 0.0000 1621518998.7711 0.0000 1621518998.7711
> 1621518998.7711 0.0000 1068070321.3518 1083644535.1382
> 421875.0000 1068070321.3518 1083644535.1382
>
>
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