From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Tue Nov 06 2007 - 15:11:04 CST
Hi Guys,
I am trying to do a NAMD run on an RNA molecule. Based on advice
received on this list, I solvated the RNA and prepared for analysis
following the NAMD ubiquitin in a water box tutorial. The only
differences were the following:
1. I changed the molecule, using an RNA instead of ubiquitin.
2. I changed the topology input file in ubq.pgn, and added some
aliases:
topology /Users/samuelflores/tbss.work/param/toppar/toppar_history/
c26b1_b2_c27a1_a2/top_all22_prot_na.inp
alias residue G GUA
alias residue C CYT
alias residue A ADE
alias residue U URA
3. I changed the following line in the ubq_wb_eq.conf file:
parameters /Users/samuelflores/tbss.work/param/toppar/
toppar_history/c26b1_b2_c27a1_a2/par_all22_prot_na.inp
..However the analysis hangs. Can anyone tell me what I'm doing
wrong? It would be much appreciated. The following is the output
from my namd2 run..
clark-alt-wi-2:~/tbss.work/1-3-box samuelflores$ /Users/samuelflores/
Desktop/NAMD_2.6_MacOSX-i686/namd2 ubq_wb_eq.conf
Charm++: standalone mode (not using charmrun)
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.6 for MacOSX-i686
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 50900 for net-darwin-x86-smp
Info: Built Wed Aug 30 12:54:31 CDT 2006 by jim on juneau.ks.uiuc.edu
Info: 1 NAMD 2.6 MacOSX-i686 1 clark-alt-wi-2.stanford.edu
samuelflores
Info: Running on 1 processors.
Info: 38572 kB of memory in use.
Info: Memory usage based on ps
Info: Configuration file is ubq_wb_eq.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 42 0 0
Info: PERIODIC CELL BASIS 2 0 44 0
Info: PERIODIC CELL BASIS 3 0 0 47
Info: PERIODIC CELL CENTER 31 29 17.5
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
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 ubq_wb_eq.dcd
Info: DCD FREQUENCY 250
Info: DCD FIRST STEP 250
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME ubq_wb_eq.xst
Info: XST FREQUENCY 250
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME ubq_wb_eq
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ubq_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 32 32 32
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_MacOSX-i686.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_MacOSX-i686.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 1194381924
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../common/ubq_wb.pdb
Info: STRUCTURE FILE ../common/ubq_wb.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS /Users/samuelflores/tbss.work/param/
toppar/toppar_history/c26b1_b2_c27a1_a2/par_all22_prot_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 226 BONDS
Info: 556 ANGLES
Info: 664 DIHEDRAL
Info: 65 IMPROPER
Info: 0 CROSSTERM
Info: 105 VDW
Info: 11 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 6232 ATOMS
Info: 4167 BONDS
Info: 2129 ANGLES
Info: 92 DIHEDRALS
Info: 6 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 6203 RIGID BONDS
Info: 12493 DEGREES OF FREEDOM
Info: 2092 HYDROGEN GROUPS
Info: TOTAL MASS = 37584 amu
Info: TOTAL CHARGE = -1 e
Info: *****************************
Info: Entering startup phase 0 with 40324 kB of memory in use.
Info: Entering startup phase 1 with 40324 kB of memory in use.
Info: Entering startup phase 2 with 40680 kB of memory in use.
Info: Entering startup phase 3 with 40732 kB of memory in use.
Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0885989 -0.128149 -0.083597
Info: LARGEST PATCH (0) HAS 1050 ATOMS
Info: CREATING 873 COMPUTE OBJECTS
Info: Entering startup phase 4 with 41448 kB 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: Entering startup phase 5 with 41584 kB of memory in use.
Info: Entering startup phase 6 with 41584 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 41584 kB of memory in use.
Info: CREATING 873 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-23 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.40436e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.10282e-22 AT 11.9138
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.56912e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-32 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138
Info: Entering startup phase 8 with 42396 kB of memory in use.
Info: Finished startup with 43548 kB of memory in use.
TCL: Minimizing for 100 steps
PRESSURE: 0 nan nan nan nan nan nan nan nan nan
GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 5201.4642 -99999999.9999 7.6139
-99999999.9999 -22105.7984 99999999.9999
0.0000 0.0000 0.0000 -99999999.9999
0.0000 -99999999.9999 -99999999.9999 0.0000
-99999999.9999 -99999999.9999 86856.0000 -99999999.9999
-99999999.9999
OPENING EXTENDED SYSTEM TRAJECTORY FILE
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
^[^C
clark-alt-wi-2:~/tbss.work/1-3-box samuelflores$
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