[Fri Sep 15 14:03:57 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/527/pcff+.frc md5 sum: 271FB553B535FE0449E31A6F8A0898D3 MedeA version 3.6.0 #------------------------------------------------------------------------------- # This calculation has 2 stages #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 atm Stage 2: This LAMMPS calculation has 6 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/527/pcff+.frc) Current system formula: K40Na696Li7Mg151S31Cl983O2936H5624 (K40Na696Li7Mg151S31Cl983O2936H5624) The nonbond terms are handled with a cutoff at 12 Angstrom. The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001. The long-range van der Waals interactions are included via tail corrections. Stage 2.2: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 1000 Maximum number of force evaluations: 10000 Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K Stage 2.5: NVT integration for 5 ns with a timestep of 1 fs T is 298.2 K Stage 2.6: Surface tension calculation using NVT integration for 2 ns with a timestep of 1 fs, T is 298.2 K #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 atm Stage 2: This LAMMPS calculation has 6 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR: Too many groups (../group.cpp:159) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/527/pcff+.frc) Current system formula: K40Na696Li7Mg151S31Cl983O2936H5624 (K40Na696Li7Mg151S31Cl983O2936H5624) The nonbond terms are handled with a cutoff at 12 Angstrom. The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001. The long-range van der Waals interactions are included via tail corrections. Stage 2.2: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 1000 Maximum number of force evaluations: 10000 Note: 2.2_Minimization.out contains warning messages from LAMMPS - examine this file for additional information. The minimization finished after 33 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 33 Initial Fmax: 15135.7 kJ/mol/Ang Fmax: 24161.6 kJ/mol/Ang Initial Frms: 950.9 kJ/mol/Ang Frms: 407.6 kJ/mol/Ang P: 11300.1 atm V: 129127.0 Ang^3 rho: 1.4116 g/mL Sxx: -12850.0 atm Syy: -11301.2 atm Szz: -9749.0 atm Syz: 279.7 atm Sxz: 31.0 atm Sxy: -654.2 atm Initial Epot: 24343.7 kJ/mol Epot: -944734.0 kJ/mol a: 32.7352 Ang b: 32.7352 Ang c: 120.5000 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: -0.1 kJ/mol/Ang sum_fy: 0.2 kJ/mol/Ang sum_fz: 59.5 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.27 +/- 0.19 K 0 0.0% P: 588.2 +/- 9.3 atm 0 0.0% V: 129127 +/- 0 Ang^3 0 0.0% rho: 1.41163 +/- 0 g/mL 0 0.0% Etotal: -1050000 +/- 200 kJ/mol 0 0.0% Epot: -1076580 +/- 180 kJ/mol 0 0.0% Ekin: 26572 +/- 17 kJ/mol 0 0.0% Evdw: 123782 +/- 48 kJ/mol 0 0.0% Ecoul: -1200850 +/- 180 kJ/mol 0 0.0% Sxx: -813 +/- 11 atm 0 0.0% Syy: -804 +/- 14 atm 0 0.0% Szz: -148 +/- 18 atm 0 0.0% Syz: -2 +/- 12 atm 0 0.0% Sxz: -1.5 +/- 9.9 atm 0 0.0% Sxy: 4 +/- 10 atm 0 0.0% Stage 2.5: NVT integration for 5 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: fs Error with T: The run is not long enough to analyze. Sorry! Error with P: The run is not long enough to analyze. Sorry! Error with V: The run is not long enough to analyze. Sorry! Error with rho: The run is not long enough to analyze. Sorry! Error with Etotal: The run is not long enough to analyze. Sorry! Error with Epot: The run is not long enough to analyze. Sorry! Error with Ekin: The run is not long enough to analyze. Sorry! Error with Evdw: The run is not long enough to analyze. Sorry! Error with Ecoul: The run is not long enough to analyze. Sorry! Error with Sxx: The run is not long enough to analyze. Sorry! Error with Syy: The run is not long enough to analyze. Sorry! Error with Szz: The run is not long enough to analyze. Sorry! Error with Syz: The run is not long enough to analyze. Sorry! Error with Sxz: The run is not long enough to analyze. Sorry! Error with Sxy: The run is not long enough to analyze. Sorry! Error in stage md-lammps-stage-0cabad5a-b476-45b6-8c17-e0ab65bbc4e7 analyze: domain error: argument not in valid range domain error: argument not in valid range while executing "expr {$s_eab/$nvals}" (object "::groupInteractions0" method "::MD::Analysis::GroupInteractions::analyze" body line 65) invoked from within "$myObjects($id) analyze" (object "::analyses1" method "::MD::Analysis::Analyses::analyze" body line 3) invoked from within "$myAnalyses analyze" (object "::nVT0" method "::MD::LAMMPS::Stage::Base::analyze" body line 169) invoked from within "chain $system" (object "::nVT0" method "::MD::LAMMPS::Stage::NVT::analyze" body line 5) invoked from within "::nVT0 analyze {}" ("eval" body line 1) invoked from within "eval ::nVT0 $args" (procedure "md-lammps-stage-0cabad5a-b476-45b6-8c17-e0ab65bbc4e7" line 1) invoked from within "$stage analyze $sys" Entire job completed on Fri 15 September 2023 at 22:36:36 CST after 30751 s (8:32:31) and running 1 tasks.