From: Tue Boesen (alyflex_at_gmail.com)
Date: Thu Mar 03 2022 - 18:03:53 CST
Thank you for the prompt reply Brian!
Given that it is only a few hundred pdbs out of about 300k pdbs that I
encounter this problem in, what you are suggesting should be possible.
However, I have two questions:
1. What exactly is the number of allowed atoms/residues in namd? Is it
the same as the number allowed in a normal pdb files? (999999 atoms and
99999 residues) I need this information such that I can proactively and
automatically change the file format for the files that need it.
2. I am not finding a lot of information on how to convert pdbs to
binary files for namd input. Would you mind elaborating on what my options
might be for that? Or linking me some material on this?
https://www.ks.uiuc.edu/Research/namd/2.10/ug/node11.html details the
binary format used by namd on output, but I can't find anything specifying
what kind of binary input file I can pass to namd? Is it the same format?
and do I just pass it directly instead of a pdb file, thus changing the
line:
coordinates sample.pdb
to
coordinates sample.binary
in the namd configuration file
Cheers
Tue
On Thu, Mar 3, 2022 at 3:14 PM Bennion, Brian <bennion1_at_llnl.gov> wrote:
> 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.
> Use +auto-provision to fully subscribe resources or +p1 to
> silence this message.
> 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/
> <https://urldefense.com/v3/__https://urldefense.us/v3/__http:/*www.ks.uiuc.edu/Research/namd/__;!!G2kpM7uM-TzIFchu!lhyuqZA3VXOYMJBUvDDswhgA86ustwSai1uTKxYxah7bjZE9gAp9bSoknOwGEz_-$__;Lw!!DZ3fjg!rDm0gUtYuM7NopH8ikgx_NxcPxDB_XeDRSalaTHAPlmq5pltFVurjSZm-OfZ9joS9g$ >
> 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$__;Lw!!DZ3fjg!rDm0gUtYuM7NopH8ikgx_NxcPxDB_XeDRSalaTHAPlmq5pltFVurjSZm-OcvUbJurQ$ >
> 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
>
> TCL: Minimizing for 100 steps
> FATAL ERROR: patch has 73608 atoms, maximum allowed is 65535
> [Partition 0][Node 0] End of program
>
>
>
>
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