Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Mon Feb 22 2010 - 01:31:07 CST

Hi George,

I am running namd2.7b2 (the CVS code from September 2009) with the amber
force field and I don't see any problem.

What makes you think its the amber force field the cause of the problem
? Does the same simulation run with another force field ?

Vlad

George Madalin Giambasu wrote:
> Hi Everybody,
>
>
> has anyone tried to run namd 2.7b2 or later with amber force field (in
> amber prmtop format) lately?
>
> For a large variety of systems (solvated/unsolvated,
> periodic/non-periodic) and machines I keep getting a segementation
> fault during the startup phase. See bellow.
>
> Versions 2.6 or 2.7b1 do not cause this problem.
>
> Thanks in advance for any tip,
>
>
> George
>
> -------------------------------------------------
> output from 2.7b2:
> -------------------------------------------------
>
> 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 CVS for Linux-x86_64
> 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-x86_64-iccstatic
> Info: Built Sat Feb 20 02:12:33 CST 2010 by jim on lisboa.ks.uiuc.edu
> Info: 1 NAMD CVS Linux-x86_64 Info: Running on 1 processors.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.0106549 s
> Info: 1.49818 MB of memory in use based on CmiMemoryUsage
> Info: Configuration file is namd_0.inp
> TCL: Suspending until startup complete.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 200
> Info: STEPS PER CYCLE 10
> Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
> Info: LDB PERIOD 2000 steps
> Info: FIRST LDB TIMESTEP 50
> Info: LAST LDB TIMESTEP -1
> Info: LDB BACKGROUND SCALING 1
> Info: HOM 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 0
> Info: CENTER OF MASS MOVING INITIALLY? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 0.833333
> Info: DCD FILENAME fep.dcd
> Info: DCD FREQUENCY 1000
> Info: DCD FIRST STEP 1000
> Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME fep
> Info: BINARY OUTPUT FILES WILL BE USED
> Info: RESTART FILENAME fep.restart
> Info: RESTART FREQUENCY 5000
> Info: BINARY RESTART FILES WILL BE USED
> Info: CUTOFF 99
> Info: PAIRLIST DISTANCE 99
> 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
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 101.5
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS 50
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 200
> Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> 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 : 0.0005
> Info: MAX ITERATIONS : 100
> Info: RIGID WATER USING SETTLE ALGORITHM
> Info: RANDOM NUMBER SEED 1266795610
> Info: USE HYDROGEN BONDS? NO
> Info: Using AMBER format force field!
> Info: AMBER PARM FILE test.parm7
> Info: AMBER COORDINATE FILE test.crd
> Info: Exclusions will be read from PARM file!
> Info: SCNB (VDW SCALING) 2
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Reading parm file (test.parm7) ...
> PARM file in AMBER 7 format
> Info: SUMMARY OF PARAMETERS:
> Info: 20 BONDS
> Info: 36 ANGLES
> Info: 28 DIHEDRAL
> Info: 0 IMPROPER
> Info: 0 CROSSTERM
> Info: 0 VDW
> Info: 55 VDW_PAIRS
> Info: TIME FOR READING PDB FILE: 1.09673e-05
> Info:
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 32 ATOMS
> Info: 34 BONDS
> Info: 58 ANGLES
> Info: 120 DIHEDRALS
> Info: 0 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 168 EXCLUSIONS
> Info: 13 RIGID BONDS
> Info: 83 DEGREES OF FREEDOM
> Info: 19 HYDROGEN GROUPS
> Info: 3 ATOMS IN LARGEST HYDROGEN GROUP
> Info: 19 MIGRATION GROUPS
> Info: 3 ATOMS IN LARGEST MIGRATION GROUP
> Info: TOTAL MASS = 267.254 amu
> Info: TOTAL CHARGE = 7.45058e-08 e
> Info: *****************************
> Info:
> Info: Entering startup at 0.0290091 s, 1.63704 MB of memory in use
> Info: Startup phase 0 took 0.000170946 s, 1.63713 MB of memory in use
> Segmentation fault
>
>
> -------------------------------------------------
> output from 2.7b1:
> -------------------------------------------------
>
> Charm++: standalone mode (not using charmrun)
> Charm++> cpu topology info is being gathered!
> Charm++> 1 unique compute nodes detected!
> Info: NAMD 2.7b1 for Linux-x86_64
> 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 60100 for net-linux-x86_64-iccstatic
> Info: Built Mon Mar 23 02:40:42 CDT 2009 by jim on belfast.ks.uiuc.edu
> Info: 1 NAMD 2.7b1 Linux-x86_64 1 Info: Running on 1 processors.
> Info: Charm++/Converse parallel runtime startup completed at 0.00889206 s
> Info: 1.50023 MB of memory in use based on CmiMemoryUsage
> Info: Configuration file is namd_0.inp
> TCL: Suspending until startup complete.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 200
> Info: STEPS PER CYCLE 10
> Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
> Info: LDB PERIOD 2000 steps
> Info: FIRST LDB TIMESTEP 50
> Info: LAST LDB TIMESTEP -1
> Info: LDB BACKGROUND SCALING 1
> Info: HOM 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 0
> Info: CENTER OF MASS MOVING INITIALLY? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 0.833333
> Info: DCD FILENAME fep.dcd
> Info: DCD FREQUENCY 1000
> Info: DCD FIRST STEP 1000
> Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME fep
> Info: BINARY OUTPUT FILES WILL BE USED
> Info: RESTART FILENAME fep.restart
> Info: RESTART FREQUENCY 5000
> Info: BINARY RESTART FILES WILL BE USED
> Info: CUTOFF 99
> Info: PAIRLIST DISTANCE 99
> 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
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 101.5
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS 50
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 200
> Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> 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 : 0.0005
> Info: MAX ITERATIONS : 100
> Info: RIGID WATER USING SETTLE ALGORITHM
> Info: RANDOM NUMBER SEED 1266796666
> Info: USE HYDROGEN BONDS? NO
> Info: Using AMBER format force field!
> Info: AMBER PARM FILE test.parm7
> Info: AMBER COORDINATE FILE test.crd
> Info: Exclusions will be read from PARM file!
> Info: SCNB (VDW SCALING) 2
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Reading parm file (test.parm7) ...
> PARM file in AMBER 7 format
> Info: SUMMARY OF PARAMETERS:
> Info: 20 BONDS
> Info: 36 ANGLES
> Info: 28 DIHEDRAL
> Info: 0 IMPROPER
> Info: 0 CROSSTERM
> Info: 0 VDW
> Info: 55 VDW_PAIRS
> Info: TIME FOR READING PDB FILE: 9.05991e-06
> Info:
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 32 ATOMS
> Info: 34 BONDS
> Info: 58 ANGLES
> Info: 120 DIHEDRALS
> Info: 0 IMPROPERS
> Info: 0 CROSSTERMS
> Info: 168 EXCLUSIONS
> Info: 13 RIGID BONDS
> Info: 83 DEGREES OF FREEDOM
> Info: 19 HYDROGEN GROUPS
> Info: TOTAL MASS = 267.254 amu
> Info: TOTAL CHARGE = 7.45058e-08 e
> Info: *****************************
> Info:
> Info: Entering startup at 0.0206242 s, 1.6342 MB of memory in use
> Info: Startup phase 0 took 9.29832e-05 s, 1.63429 MB of memory in use
> Info: Startup phase 1 took 0.000417948 s, 1.64842 MB of memory in use
> Info: Startup phase 2 took 9.29832e-05 s, 1.65178 MB of memory in use
> Info: PATCH GRID IS 1 BY 1 BY 1
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0 0 0
> Info: LARGEST PATCH (0) HAS 32 ATOMS
> Info: CREATING 11 COMPUTE OBJECTS
> Info: Startup phase 3 took 0.00030899 s, 1.68639 MB of memory in use
> Info: Startup phase 4 took 5.50747e-05 s, 1.68626 MB of memory in use
> Info: Startup phase 5 took 5.88894e-05 s, 1.68614 MB of memory in use
> LDB: Measuring processor speeds ... Done.
> Info: Startup phase 6 took 0.00012207 s, 1.68755 MB of memory in use
> Info: CREATING 11 COMPUTE OBJECTS
> Info: useSync: 1 useProxySync: 0
> Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> Info: NONBONDED TABLE SIZE: 1153 POINTS
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.83671e-40 AT 98.6303
> Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.70398e-42 AT 98.6303
> Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 4.68386e-30 AT 98.6303
> Info: Startup phase 7 took 0.00640392 s, 2.28033 MB of memory in use
> Info: Startup phase 8 took 0.000113964 s, 2.53265 MB of memory in use
> Info: Finished startup at 0.028291 s, 2.53265 MB of memory in use
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG
>
> ENERGY: 0 2.1010 34.4807 19.7000
> 0.0000 -52.5241 21.0530 0.0000
> 0.0000 0.0000 24.8106 0.0000
> 24.8106 24.9936 0.0000
>
> ENERGY: 1 1.9859 33.5135 19.6919
> 0.0000 -52.5778 20.0761 0.0000
> 0.0000 2.1910 24.8805 26.5673
> 22.6896 25.1843 26.5673
> .......
>
>
>
>
>
>

-- 
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Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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