Running AMBER FF with NAMD 2.8-CUDA

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Oct 19 2011 - 08:14:59 CDT

Hello:
First time trying to run parm7 file with NAMD 2.8 CUDA (two GTX-570
cards that work beautifully on running .psf/.pdb). I am finding it
difficult to minimize. before trying to run my files, I started with
.prmtop/.inpcrd for DNA duplex solvated as from AMBER tutorial B1 (I
also tried the updated A1 tutorial, resulting in different number of
atoms for prmto vs inpcrd).

Here the conf file:

## AMBER on NAMD, expecting a parm7 fileNAMD input
# Minimization with no fixed atom, PME

# AMBER force field
amber on #expect to read parm7 file
parmfile ./complex_oct_Na+.prmtop #from xleap
readexclusions yes # from parm7 file
exclude scaled1-4 #1-4 interact scaled by sncb 1-3 ignored
1-4scaling 0.83333333 #for 1-4 electrostatic interaction
scnb 2.0 #1-4 vdW interactions are divided by scnb
# zeroMomentum on #remove center of mass drift due to PME
# LJcorrection on #correction to vdWenergy and virial
watermodel tip3

# input
ambercoor ./complex_oct_Na+.inpcrd #from xleap

# Approximations for nonbonded interactions
cutoff 9 #for vdW and elctrostatic interactions
switching on
switchDist 6 # < cutoff
pairListDist 11 #between pair of atoms for vdW and electrost
outputpairlists 1000
stepspercycle 10 #before reassignment to pairlist
nonbondedfreq 1 #for short range
fullelectfrequency 1 #number of timesteps between electr evaluation
margin 5

# Integrator
timestep 0.1
rigidBonds all #with H needed for 2fs/step
# rigidIteractions 100 #shake max iteractions
# rigidBonds water # if 1fs/step
rigidTolerance 1e-08
useSettle on #faster than shake for water

# Output
outputName ./min-01
restartName ./min-01.rst
binaryOutput off
binaryRestart on
outputEnergies 100
restartFreq 100
DCDfile ./min-01.dcd
DCDfreq 100
XSTfile ./min-01.xst
XSTfreq 100

temperature 0

# Constant Temperature Control is off
langevin off

# Constant Pressure Control is off
langevinPiston off

# PME settings
PME on
PMETolerance 1.0e-6
PMEInterpOrder 4 # i.e. cubic spline
PMEGridSizeX 79 #size of fftw grid on x dimension
PMEGridSizeY 79
PMEGridSizeZ 79
PMEGridSpacing 1.0

# cubic periodic cell
cellBasisVector1 53.19 0. 0. #periodic cell vector1
cellBasisVector2 0. 60.13 0.
cellBasisVector3 0. 0. 62.5
cellOrigin 26.7078 26.3666 26.47117

## execution
minimize 1000
***********************

Here the log file:

Charm++> cpu topology info is gathered in 0.002 seconds.
Info: NAMD CVS-2011-06-04 for Linux-x86_64-CUDA
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60303 for net-linux-x86_64-iccstatic
Info: Built Sat Jun 4 02:22:51 CDT 2011 by jim on lisboa.ks.uiuc.edu
Info: 1 NAMD CVS-2011-06-04 Linux-x86_64-CUDA 6 gig64 francesco
Info: Running on 6 processors, 6 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00875306 s
Pe 4 sharing CUDA device 0 first 0 next 0
Pe 4 physical rank 4 binding to CUDA device 0 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Pe 1 sharing CUDA device 1 first 1 next 3
Pe 1 physical rank 1 binding to CUDA device 1 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Did not find +devices i,j,k,... argument, using all
Pe 0 sharing CUDA device 0 first 0 next 2
Pe 0 physical rank 0 binding to CUDA device 0 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Pe 3 sharing CUDA device 1 first 1 next 5
Pe 3 physical rank 3 binding to CUDA device 1 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Pe 5 sharing CUDA device 1 first 1 next 1
Pe 5 physical rank 5 binding to CUDA device 1 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Pe 2 sharing CUDA device 0 first 0 next 4
Pe 2 physical rank 2 binding to CUDA device 0 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Info: 1.64146 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is min-01.conf
Info: Working in the current directory /home/francesco/trial
TCL: Suspending until startup complete.
Info: Using TIP3P water model.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 0.1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 53.19 0 0
Info: PERIODIC CELL BASIS 2 0 60.13 0
Info: PERIODIC CELL BASIS 3 0 0 62.5
Info: PERIODIC CELL CENTER 26.7078 26.3666 26.4712
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
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: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 0.833333
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME ./min-01.dcd
Info: DCD FREQUENCY 100
Info: DCD FIRST STEP 100
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME ./min-01.xst
Info: XST FREQUENCY 100
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME ./min-01
Info: RESTART FILENAME ./min-01.rst
Info: RESTART FREQUENCY 100
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 6
Info: SWITCHING OFF 9
Info: PAIRLIST DISTANCE 11
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLIST OUTPUT STEPS 1000
Info: PAIRLISTS ENABLED
Info: MARGIN 5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 18.5
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.348832
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 79 79 79
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from
FFTW_NAMD_CVS-2011-06-04_Linux-x86_64-CUDA.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_CVS-2011-06-04_Linux-x86_64-CUDA.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
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 1319029589
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE ./complex_oct_Na+.prmtop
Info: AMBER COORDINATE FILE ./complex_oct_Na+.inpcrd
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 (./complex_oct_Na+.prmtop) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 58685 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 58 BONDS
Info: 123 ANGLES
Info: 58 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 210 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PDB FILE: 3.09944e-06
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 211793 ATOMS
Info: 211907 BONDS
Info: 66454 ANGLES
Info: 128063 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 372820 EXCLUSIONS
Info: 195464 RIGID BONDS
Info: 439912 DEGREES OF FREEDOM
Info: 75014 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 75014 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 1.29231e+06 amu
Info: TOTAL CHARGE = -0.00114355 e
Info: MASS DENSITY = 10.7355 g/cm^3
Info: ATOM DENSITY = 1.05952 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 3.74494 s, 61.7201 MB of memory in use
Info: Startup phase 0 took 0.000406027 s, 61.7165 MB of memory in use
Info: Startup phase 1 took 1.15685 s, 94.3063 MB of memory in use
Info: Startup phase 2 took 0.06902 s, 95.9572 MB of memory in use
Info: Startup phase 3 took 0.000153065 s, 95.9563 MB of memory in use
Info: PATCH GRID IS 2 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (12) HAS 13539 ATOMS
Info: Startup phase 4 took 0.100487 s, 125.014 MB of memory in use
Info: PME using 6 and 6 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3 4 5
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 5 took 1.39518 s, 125.697 MB of memory in use
Info: Startup phase 6 took 0.0369661 s, 102.8 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 1.21179 s, 100.046 MB of memory in use
Info: CREATING 408 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: Updated CUDA LJ table with 20 x 20 elements.
Info: Updated CUDA force table with 4096 elements.
Info: Found 419 unique exclusion lists needing 1496 bytes
Info: Startup phase 8 took 0.120829 s, 102.348 MB of memory in use
Info: Startup phase 9 took 0.000133038 s, 102.726 MB of memory in use
Info: Finished startup at 7.83675 s, 102.726 MB of memory in use

TCL: Minimizing for 1000 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
       KINETIC TOTAL TEMP POTENTIAL
  TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG

ENERGY: 0 21108.3749 13444.9074 17715.4597
0.0000 -1046653.4155 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 199894.6687 9999999999.9999 9999999999.9999

OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 94018 ATOMS WITH BAD CONTACTS DOWNHILL

After unusually long time, clashes were not removed. Is there any
conflict in the input file?

Thanks
francesco pietra

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