From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Tue May 11 2010 - 15:38:14 CDT
Hi Liu,
I am writing to let you know that your suggestion was excellent.
Thinking on your suggestion that could be an infinite loop calculation, I made a little change on PBC values. It works on namd v2.7b.
I also used the original script (conf file) running namd v2.6 in another macchine. It also works.
Many thanks for your help.
Flavio Seixas
--- On Sun, 5/9/10, Bo Liu <boliu_at_ks.uiuc.edu> wrote:
From: Bo Liu <boliu_at_ks.uiuc.edu>
Subject: Re: namd-l: Timestep 594
To: "flavio seixas" <oivalf_nix_at_yahoo.com>
Cc: namd-l_at_ks.uiuc.edu
Date: Sunday, May 9, 2010, 5:28 PM
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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