From: Giovanni Nico (g.nico_at_ba.iac.cnr.it)
Date: Tue Jun 15 2010 - 11:51:08 CDT
Dear NAMD users,
I just started using NAMD. I installed the version 2.7b2 on a
64 bit machine (ubutu operative system).
I successfully ran a configuration file taken from tutorial files. Then,
to learn more about
the use of the AMBER field I replaced the commands
> coordinates <..>.pdb
> structure <..>.psf
> parameters par_all27_prot_lipid_na.inp
> paratypecharmm on
with the following ones
> amber yes
> parmfile <...>.prmtop #AMBER topology
> ambercoor <...>.prmcrd #coordinates
>
I created prmtop and coordinate files via
> XLEAP from AmberTools. I used the following commands
>
> source leaprc.ff99SB
> loadPdb heating_example.pdb
> saveAmberParm x prmtop prmcrd
Unfortunately, I got a SEGMENTATION FAULT message (see text after the
CUT HERE at the end of this message!)
Did I some mistakes when installing NAMD?
Is this related to the NAMD version (2.7b2 on a 64 bit machine?)
Did I need to properly set a parameter to use AMBER?
Is this related to the usage of AMBER commands?
Is there any other possible explanation?
Thank you for your help!
regards,
giovanni
================================ CUT HERE
====================================
Charm++: standalone mode (not using charmrun)
Charm++> cpu topology info is being gathered.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Info: NAMD 2.7b2 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 Thu Nov 12 22:12:21 CST 2009 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.7b2 Linux-x86_64 1 quad2-desktop rocco
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00371122 s
Info: 1.50945 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is min.conf
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuation file but were not needed
Warning: switchdist
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 2000
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 83.04 0 0
Info: PERIODIC CELL BASIS 2 0 70.67 0
Info: PERIODIC CELL BASIS 3 0 0 60.45
Info: PERIODIC CELL CENTER 43.2187 36.528 31.4622
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
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: 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 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 0.83333
Info: DCD FILENAME outputs/1hjn3_min.coor.dcd
Info: DCD FREQUENCY 2000
Info: DCD FIRST STEP 2000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME outputs/1hjn3_min.xst
Info: XST FREQUENCY 2000
Info: VELOCITY DCD FILENAME outputs/1hjn3_min.vel.dcd
Info: VELOCITY DCD FREQUENCY 2000
Info: VELOCITY DCD FIRST STEP 2000
Info: OUTPUT FILENAME outputs/1hjn3_min
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME outputs/1hjn3_min.rst
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 12
Info: PAIRLIST DISTANCE 12
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 14.5
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: MOMENTUM OUTPUT STEPS 1000
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 1000
Info: CONJUGATE GRADIENT MINIMIZATION ACTIVE
Info: LINE MINIMIZATION GOAL = 0.001
Info: BABY STEP SIZE = 0.01
Info: TINY STEP SIZE = 1e-06
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 84 70 60
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b2_Linux-x86_64.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-x86_64.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-05
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1276619587
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE 1hjn3.prmtop
Info: AMBER COORDINATE FILE em2.rst
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 (1hjn3.prmtop) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 9992 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 35 BONDS
Info: 66 ANGLES
Info: 35 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 153 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 3.8147e-06
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 31682 ATOMS
Info: 31700 BONDS
Info: 3068 ANGLES
Info: 5926 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 39178 EXCLUSIONS
Info: 30797 RIGID BONDS
Info: 64246 DEGREES OF FREEDOM
Info: 10877 HYDROGEN GROUPS
Info: TOTAL MASS = 192680 amu
Info: TOTAL CHARGE = -3.4658e-06 e
Info: MASS DENSITY = 0.901939 g/cm^3
Info: ATOM DENSITY = 0.0893087 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 0.150035 s, 9.55043 MB of memory in use
Info: Startup phase 0 took 2.5034e-05 s, 9.55052 MB of memory in use
Segmentation fault
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