Charm++> Running on MPI version: 3.1 Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE) Charm++> Running in non-SMP mode: 48 processes (PEs) Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.10.1-0-gcc60a79-namd-charm-6.10.1-build-2020-Mar-05-18422 Charm++> MPI timer is synchronized CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 hosts (2 sockets x 24 cores x 2 PUs = 96-way SMP) Charm++> cpu topology info is gathered in 0.043 seconds. Info: NAMD 2.14b2 for Linux-x86_64-MPI 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 61001 for mpi-linux-x86_64 Info: Built Tue Jul 14 00:15:02 UTC 2020 by sbekele on koehr02 Info: 1 NAMD 2.14b2 Linux-x86_64-MPI 48 r3i3n5 sbekele Info: Running on 48 processors, 48 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0871058 s Info: 272.75 MB of memory in use based on /proc/self/stat Info: Configuration file is /p/work1/sbekele/6430921/namd/step3_mini.inp Info: Changed directory to /p/work1/sbekele/6430921/namd TCL: Suspending until startup complete. Warning: Setting water model to 'swm4' (SWM4-DP) for Drude polarization. Info: SIMULATION PARAMETERS: Info: TIMESTEP 0.1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 120 0 0 Info: PERIODIC CELL BASIS 2 0 120 0 Info: PERIODIC CELL BASIS 3 0 0 120 Info: PERIODIC CELL CENTER 0 0 -0.0316244 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING ALL CLUSTERS 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: INITIAL TEMPERATURE 303.15 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 ELECTROSTATICS SCALED BY 1 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: DCD FILENAME step3_mini.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 1000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME step3_mini.xst Info: XST FREQUENCY 1000 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME step3_mini Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME step3_mini.restart Info: RESTART FREQUENCY 500 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 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: PAIRLISTS ENABLED Info: MARGIN 0.555 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19.055 Info: ENERGY OUTPUT STEPS 125 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: COLLECTIVE VARIABLES CALCULATION REQUESTED Info: COLLECTIVE VARIABLES CONFIGURATION step3_mini.col Info: DRUDE MODEL DUAL THERMOSTAT IS ACTIVE Info: DRUDE BOND TEMPERATURE 1 Info: DRUDE DAMPING COEFFICIENT IS 20 INVERSE PS Info: DRUDE HARD WALL RESTRAINT IS ACTIVE FOR DRUDE BONDS Info: DRUDE MAXIMUM BOND LENGTH BEFORE RESTRAINT IS 0.2 Info: DRUDE NBTHOLE IS ACTIVE Info: DRUDE NBTHOLE RADIUS IS 5 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 303.15 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 1 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 50 FS Info: DECAY TIME IS 25 FS Info: PISTON TEMPERATURE IS 303.15 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 0.257952 Info: PME INTERPOLATION ORDER 6 Info: PME GRID DIMENSIONS 120 120 120 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from system Info: Attempting to read FFTW data from FFTW_NAMD_2.14b2_Linux-x86_64-MPI_FFTW3.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.14b2_Linux-x86_64-MPI_FFTW3.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 1594687255 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../step2_drude.pdb Info: STRUCTURE FILE ../step2_drude.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ../toppar_drude/toppar_drude_master_protein_2019g.str Info: PARAMETERS ../toppar_drude/toppar_drude_lipid_2017c.str Info: PARAMETERS ../toppar_drude/toppar_drude_model_2019g.str Info: PARAMETERS ../toppar_drude/toppar_drude_carbohydrate_2019a.str Info: PARAMETERS ../toppar_drude/toppar_drude_nucleic_acid_2017c.str Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Info: SUMMARY OF PARAMETERS: Info: 435 BONDS Info: 986 ANGLES Info: 3112 DIHEDRAL Info: 111 IMPROPER Info: 10 CROSSTERM Info: 173 VDW Info: 343 VDW_PAIRS Info: 38 NBTHOLE_PAIRS Warning: Ignored 104538 bonds with zero force constants. Warning: Will get H-H distance in rigid H2O from H-O-H angle. Warning: Ignored 53760 bonds with lone pairs. Warning: Will infer lonepair bonds from LPhost entries. Warning: Ignored 55728 bonds with Drude particles. Warning: Will use polarizability to assign Drude bonds. Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE USED Info: TIME FOR READING PSF FILE: 1.99837 Info: Reading pdb file ../step2_drude.pdb Info: TIME FOR READING PDB FILE: 0.295384 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 270518 ATOMS Info: 219191 BONDS Info: 64162 ANGLES Info: 16293 DIHEDRALS Info: 1712 IMPROPERS Info: 379 CROSSTERMS Info: 0 EXCLUSIONS Info: 156021 RIGID BONDS Info: 53819 LONE PAIRS Info: 55728 DRUDE ATOMS Info: 494076 DEGREES OF FREEDOM Info: 326892 DRUDE COM DEGREES OF FREEDOM Info: 167184 DRUDE BOND DEGREES OF FREEDOM Info: 55728 HYDROGEN GROUPS Info: 5 ATOMS IN LARGEST HYDROGEN GROUP Info: 53183 MIGRATION GROUPS Info: 15 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 996274 amu Info: TOTAL CHARGE = 1.82074e-05 e Info: MASS DENSITY = 0.957402 g/cm^3 Info: ATOM DENSITY = 0.15655 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 2.8726 s, 445.48 MB of memory in use Info: Startup phase 0 took 0.00324038 s, 445.48 MB of memory in use FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs FATAL ERROR: must have same number of LP hosts as lone pairs Info: ADDED 653018 IMPLICIT EXCLUSIONS [Partition 0][Node 0] End of program Dear NAMD developers and users, I recently downloaded the NAMD package and installed it with mpi. When I try to run, I got the error message FATAL ERROR: must have same number of LP hosts as lone pairs I tried to look it up in the NAMD mailing list in case somebody had laready encountered a similar issue but did not find a solution. So, I searched in the source code where the error message is printed and found out that it is in: NAMD_2.14b2_Source/Linux-x86_64-g++/src/Molecule.C =============== Lines 9454-9457 =============== if (is_lonepairs_psf && numLonepairs != numLphosts) { NAMD_die("must have same number of LP hosts as lone pairs"); } A print out of "numZeroMassAtoms" after the loop containing the lines below shows that the number of zero mass atoms is correctly calculated: =============== Lines 1383-1387 =============== /* Parse up the line */ read_count=sscanf(buffer, "%d %s %s %s %s %s %f %f", &atom_number, segment_name, residue_number, residue_name, atom_name, atom_type, &charge, &mass); if (mass <= 0.05) ++numZeroMassAtoms; =============== However, the number of zero mass atoms is zero when assigned to the number of lone pairs as shown below. If the number is hardwired as in the commented line, everything works fine. =============== Lines 9446-9447 =============== if (simParams->watmodel == WAT_TIP4 || is_lonepairs_psf) { //numZeroMassAtoms = 53819; // These MUST be lonepairs. numLonepairs = numZeroMassAtoms; // These MUST be lonepairs. ***************************************** Unless there is something wrong I am doing, one does not want to edit and compile for every new system. I appreciate if someone can help resolve this issue. I have attached the log file for reference. Thanks in advance, Selemon Dear NAMD developers and users, I recently downloaded the NAMD package and installed it with mpi. When I try to run, I got the error message FATAL ERROR: must have same number of LP hosts as lone pairs I tried to look it up in the NAMD mailing list in case somebody had laready encountered a similar issue but did not find a solution. So, I searched in the source code where the error message is printed and found out that it is in: NAMD_2.14b2_Source/Linux-x86_64-g++/src/Molecule.C =============== Lines 9454-9457 =============== if (is_lonepairs_psf && numLonepairs != numLphosts) { NAMD_die("must have same number of LP hosts as lone pairs"); } A print out of "numZeroMassAtoms" after the loop containing the lines below shows that the number of zero mass atoms is correctly calculated: =============== Lines 1383-1387 =============== /* Parse up the line */ read_count=sscanf(buffer, "%d %s %s %s %s %s %f %f", &atom_number, segment_name, residue_number, residue_name, atom_name, atom_type, &charge, &mass); if (mass <= 0.05) ++numZeroMassAtoms; =============== However, the number of zero mass atoms is zero when assigned to the number of lone pairs as shown below. If the number is hardwired as in the commented line, everything works fine. =============== Lines 9446-9447 =============== if (simParams->watmodel == WAT_TIP4 || is_lonepairs_psf) { //numZeroMassAtoms = 53819; // These MUST be lonepairs. numLonepairs = numZeroMassAtoms; // These MUST be lonepairs. ***************************************** Unless there is something wrong I am doing, one does not want to edit and compile for every new system. I appreciate if someone can help resolve this issue. I have attached the log file for reference. Thanks in advance, Selemon