From: Tue Boesen (alyflex_at_gmail.com)
Date: Thu Mar 03 2022 - 19:15:52 CST
Unfortunately vmd does not appear to understand the pdb from tleap as is,
but at least I have some way to investigate this now and move forward.
So thank you for your help.
Cheers
Tue
On Thu, Mar 3, 2022 at 4:18 PM Bennion, Brian <bennion1_at_llnl.gov> wrote:
> Does vmd read and understand your out of spec pdb files? If so, then
> loading into vmd and writing out in another format can be done via command
> line text commands.
>
> see the vmd manual for more info
>
> namd2.10 is a bit old at this point
>
> you would use bincoordinates
> see the namd2.12 manual for that.
>
> best
> Brian
>
> ------------------------------
> *From:* Tue Boesen <alyflex_at_gmail.com>
> *Sent:* Thursday, March 3, 2022 4:03 PM
> *To:* Bennion, Brian <bennion1_at_llnl.gov>
> *Cc:* NAMD list <namd-l_at_ks.uiuc.edu>
> *Subject:* Re: namd-l: How to handle large pdbs in namd?
>
> 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
> <https://urldefense.com/v3/__https://urldefense.us/v3/__https:/*www.ks.uiuc.edu/Research/namd/2.10/ug/node11.html__;!!G2kpM7uM-TzIFchu!h4SD0IdkDOyk_K4q8IyKaiNlth3gErPztp62vK5WoS1sJ2EHc0Q_JAk0DOOAYrmU$__;Lw!!DZ3fjg!tk98LBQm3spRg51JAwaNskw9kfFaIu-fN_RkXGA5douFbv-aqymEHNcJcsj7f7TfeA$ >
> 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_-$__;Lw!!DZ3fjg!tk98LBQm3spRg51JAwaNskw9kfFaIu-fN_RkXGA5douFbv-aqymEHNcJcsiWiojmMQ$ >
> 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$__;Lw!!DZ3fjg!tk98LBQm3spRg51JAwaNskw9kfFaIu-fN_RkXGA5douFbv-aqymEHNcJcsiZwy9bhw$ >
> 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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