Hello:
As a prelude to work with my files, I am experiencing difficulties in
minimizing .prmtop/.inpcrd from the updated A1 tutorial (duplex DNA)
by making use of NAMD 2.8-CUDA on GTX-580 cards (which operate
correctly on .psf/.pdb).
I wonder whether I have misapplied Giambasu-Case guidelines for the
truncated octahedral box or what else, for ex. does NAMD accept
.inpcrd or should .pdb be saved from leap?. The same issue " Num of
atoms in coordinate file is different from that in parm file input
.conf file" occurs also with files from my past simulations, which
were carried out totally within AMBER8, 9 or 10. On the other hand,
present .prmtop/.inpcrd, taken from A1 tutorial, load correctly on
VMD-CUDA.
The periodic boundary info to the input .conf was gived in the form:
# truncated octahedron periodic boundary conditions
set dist 62.8127420
set xx [ expr $dist ]
set xy [ expr $dist * 1/3 ]
set xz [ expr $dist * -1/3 ]
set yx [ expr 0 ]
set yy [ expr $dist * sqrt(2) * 2/3 ]
set yz [ expr $dist * sqrt(2) * 1/3 ]
set zx [ expr 0 ]
set zy [ expr 0 ]
set zz [ expr $dist * sqrt(6) * 1/3 ]
cellBasisVector1 $xx $xy $xz
cellBasisVector2 $yx $yy $yz
cellBasisVector3 $zx $zy $zz
cellOrigin 26.7078 26.3666 26.47117
where the distance was taken from the last line of .inpcrd:
62.8127420 62.8127420 62.8127420 109.4712175 109.4712175 109.4712175
while the center was taken with tcl commands
set all [atomselect top all]
measure center $all
i.e., the same way as if it were a rectangular/cubic box.
Below the output, which also shows the choice of settings:
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00910211 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
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 5 sharing CUDA device 1 first 1 next 1
Pe 2 sharing CUDA device 0 first 0 next 4
Pe 5 physical rank 5 binding to CUDA device 1 on gig64: 'GeForce GTX
580' Mem: 1535MB Rev: 2.0
Pe 2 physical rank 2 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 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
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 62.8127 20.9376 -20.9376
Info: PERIODIC CELL BASIS 2 0 59.2204 29.6102
Info: PERIODIC CELL BASIS 3 0 0 51.2864
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 1319090726
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE ./1PLC.prmtop
Info: AMBER COORDINATE FILE ./1PLC.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 (./1PLC.prmtop) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 5022 H-H bonds.
FATAL ERROR: Num of atoms in coordinate file is different from that in
parm file!
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Num of atoms in coordinate file is different from
that in parm file!
Thanks a lot for advice
francesco pietra
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Received on Thu Oct 20 2011 - 00:00:03 PDT
