From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Tue Jun 15 2010 - 14:25:13 CDT
It looks like NAMD properly reads the amber parm/top files so assuming NAMD
actually runs (you did run an example system already right?) it seems you may
have done something wrong w/ the build up of the system in tleap.
Does the structure summary for the amber.parm/top seem right? Can you load it
in VMD ? (note if it's amber parm7 or older parm format)
Have you built up the molec w/ charm topology to compare w/ AMBER?
This is useful exercise to make sure you are really setting all inputs
properly (like the scee factor)
My guess is your periodic box is wrong OR you have bad coordinate info. By bad
coord info I mean either NAMD is misreading some coordinate information so the
energy/force calcs die or there are some nasty clashes in your system and NAMD
is reading them correctly... it's just a bad structure.
Taking a look w/ VMD should help you in either case.
If you can get just 1 energy calc then it's very very likely a system
build/setup problem not a namd problem but w/out even one energy calc seems
like it could be a NAMD problem.
keep me/use posted. I 'd like to hear what you find.
Tom
On Tuesday 15 June 2010 11:51:08 am Giovanni Nico wrote:
> 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
>
*******************************
Thomas C. Bishop
Tel: 504-862-3370
Fax: 504-862-8392
http://dna.ccs.tulane.edu
********************************
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