From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Mar 03 2022 - 17:13:58 CST
Hello,
The file has overrun the number allowed for an unsigned integer in the data structures used by NAMD
Would you be able to use VMD or another tool change the file format to one of the binary formats that allow for large numbers of atoms?
brian
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Tue Boesen <alyflex_at_gmail.com>
Sent: Thursday, March 3, 2022 2:40 PM
To: NAMD list <namd-l_at_ks.uiuc.edu>
Subject: namd-l: How to handle large pdbs in namd?
Hi
I am trying to run namd on systems that are technically too large to exist in the pdb format (more than 1 million atoms and/or 100000 residues). The files went beyond those limits after they were solvated by tleap (tleap just adds extra width to those variables in the pdb and pushes everything else further to the right, which is technically not allowed in the old pdb format, but seems to work)
I can't figure out whether this is what is causing the issue in namd or whether namd is smart enough to still read these technically wrong pdbs.
The logfile with error is shown below, but essentially the error is:
FATAL ERROR: patch has 73608 atoms, maximum allowed is 65535
I tried looking up that error and adding additional patches with:
twoAwayX yes
twoAwayY yes
twoAwayZ yes
in the conf file, but that didn't change anything.
It should be noted that I have tried running this with both namd3 and namd2 and I get similar messages on both.
Further information, the system I'm trying to run in this case has 622001 atoms in it and 206601 residues. My system should have plenty of memory to handle this (64GB and 24GB on the GPU with namd3)
Any suggestions?
Cheers
Tue
Charm++> No provisioning arguments specified. Running with a single PE.
TCL: Minimizing for 100 steps
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: Tue Dec 13 2022 - 14:32:44 CST
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Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads (PEs)
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556
Warning> Randomization of virtual memory (ASLR) is turned on in the kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try running with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 hosts (1 sockets x 8 cores x 2 PUs = 16-way SMP)
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD Git-2022-02-15 for Linux-x86_64-multicore
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. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 61002 for multicore-linux-x86_64-iccstatic
Info: Built Tue Feb 15 01:57:34 CST 2022 by jmaia on titan.ks.uiuc.edu<https://urldefense.com/v3/__https://urldefense.us/v3/__http:/*titan.ks.uiuc.edu__;!!G2kpM7uM-TzIFchu!lhyuqZA3VXOYMJBUvDDswhgA86ustwSai1uTKxYxah7bjZE9gAp9bSoknHTDT7PO$__;Lw!!DZ3fjg!rvm-cSA0c8A5DJcW8F1_Qe7RCPinlXFZmA_mpCYUOdTcgOs6AmueD6B7fC6At6RRGw$ >
Info: 1 NAMD Git-2022-02-15 Linux-x86_64-multicore 1 tue-ubuntu tue
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0012051 s
CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification)
Info: 32.5156 MB of memory in use based on /proc/self/stat
Info: Configuration file is /media/tue/Data/Data/test/relax_pdb_tmp/calc/1b8t_0_0/namd/1b8t_0_0.conf
Info: Changed directory to /media/tue/Data/Data/test/relax_pdb_tmp/calc/1b8t_0_0/namd
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: paraTypeXplor (parameters)
Warning: paraTypeCharmm (parameters)
Info: Using TIP3P water model.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 155.233 0 0
Info: PERIODIC CELL BASIS 2 0 209.315 0
Info: PERIODIC CELL BASIS 3 0 0 199.126
Info: PERIODIC CELL CENTER 0.170688 0.322723 -0.0372404
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
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: EMPTY PATCH LOAD 40 ATOMS
Info: INITIAL TEMPERATURE 310
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 min1.dcd
Info: DCD FREQUENCY 200
Info: DCD FIRST STEP 200
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME min1
Info: RESTART FILENAME min1.restart
Info: RESTART FREQUENCY 200
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 10
Info: PAIRLIST DISTANCE 16
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 100
Info: PAIRLISTS ENABLED
Info: MARGIN 0.555
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 19.055
Info: ENERGY OUTPUT STEPS 200
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: MOMENTUM OUTPUT STEPS 200
Info: TIMING OUTPUT STEPS 200
Info: PRESSURE OUTPUT STEPS 200
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN USING BBK INTEGRATOR
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 200 FS
Info: DECAY TIME IS 100 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 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 160 216 200
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from /media/tue/Data/Data/FFT/FFT_160_216_200.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to /media/tue/Data/Data/FFT/FFT_160_216_200.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 1646346306
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE /media/tue/Data/Data/test/relax_pdb_tmp/calc/1b8t_0_0/leap/1b8t_0_0_neutral.prmtop
Info: COORDINATE PDB /media/tue/Data/Data/test/relax_pdb_tmp/calc/1b8t_0_0/leap/1b8t_0_0_neutral.pdb
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 (/media/tue/Data/Data/test/relax_pdb_tmp/calc/1b8t_0_0/leap/1b8t_0_0_neutral.prmtop) ...
PARM file in AMBER 7 format
Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS.
Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY.
Warning: Found 206397 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 67 BONDS
Info: 152 ANGLES
Info: 152 HARMONIC
Info: 0 COSINE-BASED
Info: 192 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 136 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: Reading pdb file /media/tue/Data/Data/test/relax_pdb_tmp/calc/1b8t_0_0/leap/1b8t_0_0_neutral.pdb
Info: TIME FOR READING PDB FILE: 0.390149
Info:
Info: LONG-RANGE LJ: APPLYING ANALYTICAL CORRECTIONS TO ENERGY AND PRESSURE
Info: LONG-RANGE LJ: AVERAGE A AND B COEFFICIENTS 576987 AND 588.695
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 622001 ATOMS
Info: 622018 BONDS
Info: 5091 ANGLES
Info: 12361 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 634422 EXCLUSIONS
Info: 620575 RIGID BONDS
Info: 1245428 DEGREES OF FREEDOM
Info: 207823 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 207823 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 3.7392e+06 amu
Info: TOTAL CHARGE = -6.47979e-06 e
Info: MASS DENSITY = 0.959678 g/cm^3
Info: ATOM DENSITY = 0.0961344 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 1.00577 s, 216.102 MB of memory in use
Info: Startup phase 0 took 5.0767e-05 s, 216.102 MB of memory in use
Info: ADDED 0 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.0809236 s, 323.727 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-22 AT 9.94673
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 5.64247e-16 AT 9.94673
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290479 AT 0.251946
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 2.11758e-22 AT 9.94673
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 5.86184e-16 AT 9.94673
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000178193 AT 9.97184
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.00974e-28 AT 9.99687
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 6.2204e-22 AT 9.99687
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.000263305 s, 323.727 MB of memory in use
Info: Startup phase 3 took 1.0521e-05 s, 323.727 MB of memory in use
Info: Startup phase 4 took 0.000226755 s, 323.727 MB of memory in use
Info: Startup phase 5 took 1.035e-05 s, 323.727 MB of memory in use
Info: PATCH GRID IS 8 (PERIODIC) BY 10 (PERIODIC) BY 10 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00444736 -0.0159901 0.00127434
Info: LARGEST PATCH (440) HAS 70095 ATOMS
Info: TORUS A SIZE 1 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0856527 s, 417.332 MB 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: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 7 took 0.00937403 s, 443.965 MB of memory in use
Info: Startup phase 8 took 1.7314e-05 s, 443.965 MB of memory in use
Info: Startup phase 9 took 1.6722e-05 s, 443.965 MB of memory in use
Info: Startup phase 10 took 8.115e-06 s, 443.965 MB of memory in use
Info: Startup phase 11 took 9.929e-06 s, 443.965 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 12 took 0.000113648 s, 443.965 MB of memory in use
Info: CREATING 16005 COMPUTE OBJECTS
Info: Startup phase 13 took 0.0218958 s, 471.918 MB of memory in use
Info: Startup phase 14 took 4.8052e-05 s, 471.918 MB of memory in use
Info: Startup phase 15 took 0.000920145 s, 572.031 MB of memory in use
Info: Finished startup at 1.20532 s, 572.031 MB of memory in use
FATAL ERROR: patch has 73608 atoms, maximum allowed is 65535
[Partition 0][Node 0] End of program