Re: Timestep 594

From: Bo Liu (boliu_at_ks.uiuc.edu)
Date: Sun May 09 2010 - 11:28:05 CDT

Hi Seixas,

Try to save the restart files at time step 500, then relaunch the
minimization starting from the coordinates of step 500.
You can also try minimize your system with NAMD 2.6.
See if it will get better.

I believe this is the reported bug which is due to an infinite loop in the
minimizer of NAMD 2.7b2, though it was supposed to be impossible to be
accessed, it turns out to be only unlikely.

You can check out the latest nightly build version of NAMD, I believe Jim
Phillips has already fixed this problem.

Cheers,
Bo

On Sun, May 9, 2010 at 9:39 AM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:

> Hi,
> I am a beginner in using NAMD.
> I search for answers at google and NAMD forum with the keywords "process
> delays" or "stop at timestep" and a lot of others. I do not find anything
> regarding this problem.
>
> I am just the only one person that user namd here at department and do not
> know another way to search for help.
>
> I´m was running a process with 1000 steps of minimization and equilibration
> on a Ubuntu Linux x86 machine.
>
> Mysteriously at step number 594, the minimization do not go on.
> The program do not stopped and the process was still running for another 48
> hours after reach 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
>
>
> Thanks for any help.
>
>
> Prof. Flavio Augusto Vicente Seixas
> Department of Biochemistry
> State University of Maringá
> MARINGÁ - PR - BRAZIL
> favseixas_at_uem.br
> oivalf_nix_at_yahoo.com
> +55 44 36219335
>
>
>
>
>
>

-- 
========================================
Bo Liu
Theoretical and Computational Biophysics Group
3027 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.ks.uiuc.edu/~boliu
========================================

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