From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Mon Feb 22 2010 - 10:50:13 CST
Yes and yes. I specified the scaling correctly and used in some of the
tests the latest (Feb 20th) cvs version.
Do you mind if I ask to try a simple (one nucleotide in vacuum, 100 MD
steps) test with your namd version? I can send you all the necessary files.
thanks for your insights,
George
Vlad Cojocaru wrote:
> HI George,
>
> I assume that you correctly specified the scaling parameters to be
> used with the amber ff.
>
> If you did that, I really cannot explain your error. Did you try the
> newest CVS code of NAMD ?
>
> Vlad
>
> George Madalin Giambasu wrote:
>> Hi Vlad,
>>
>>
>> Yes, I see the error coming when using amber prmtop files. For the
>> sake of comparison, I run the "jac1000" benchmark (it comes with namd
>> 2.6) both using the xplor psf and the amber prmtop with namd2.7b2
>> and the latest cvs version.
>>
>> The xplor version runs OK, whereas the amber prmtop gives the
>> segfault in both cases.
>>
>> Apart from that, I have few DNA and RNA systems (solvated and
>> unsolvated) that cause the same error.
>>
>>
>> G
>>
>>
>> Vlad Cojocaru wrote:
>>> 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
>>>> .......
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>
-- ________________________________________________________________________ George Madalin Giambasu PhD Student University of Minnesota Phone : (612) 625-6317 Department of Chemistry Fax : (612) 626-7541 207 Pleasant St. SE e-mail: Minneapolis, MN USA 55455-0431 GeorgeMGiambasu_at_umn.edu York Research Group giambasu_at_gmail.com http://theory.chem.umn.edu/~giambasu ________________________________________________________________________
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