[Sun Aug 06 11:57:14 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir0/405/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 5 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir0/405/pcff+.frc) Current system formula: O2000H4000 (OH2) 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: NPT integration for 2 ns with a timestep of 1 fs P is 1 atm with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed 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 5 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir0/405/pcff+.frc) Current system formula: O2000H4000 (OH2) 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 1000 steps ending because the max iterations Property Value Units ------------------ ---------- ----------- nSteps: 1000 Initial Fmax: 3970.4 kJ/mol/Ang Fmax: 15.6 kJ/mol/Ang Initial Frms: 415.1 kJ/mol/Ang Frms: 1.0 kJ/mol/Ang P: -5411.8 atm V: 59830.2 Ang^3 rho: 1.0000 g/mL Sxx: 5214.9 atm Syy: 5586.4 atm Szz: 5434.1 atm Syz: 91.0 atm Sxz: -148.5 atm Sxy: 65.0 atm Initial Epot: 123319.3 kJ/mol Epot: -118265.9 kJ/mol a: 30.0000 Ang b: 30.0000 Ang c: 66.4780 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 0.0 kJ/mol/Ang sum_fy: -0.0 kJ/mol/Ang sum_fz: -0.0 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: 298.19 +/- 0.12 K 0 0.0% P: 86.9 +/- 6.8 atm 0 0.0% V: 59830.2 +/- 1.3e-09 Ang^3 0 0.0% rho: 1 +/- 0 g/mL 0 0.0% Etotal: -75541 +/- 14 kJ/mol 0 0.0% Epot: -90414 +/- 12 kJ/mol 0 0.0% Ekin: 14872.3 +/- 6 kJ/mol 0 0.0% Evdw: 21602 +/- 14 kJ/mol 0 0.0% Ecoul: -112016 +/- 22 kJ/mol 0 0.0% Sxx: -84.4 +/- 8.5 atm 0 0.0% Syy: -91 +/- 10 atm 0 0.0% Szz: -86 +/- 11 atm 0 0.0% Syz: -2.4 +/- 5.7 atm 0 0.0% Sxz: -1.9 +/- 5.2 atm 0 0.0% Sxy: -0.5 +/- 6 atm 0 0.0% Stage 2.5: NPT integration for 2 ns with a timestep of 1 fs P is 1 atm with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.14 +/- 0.11 K 0 0.0% P: 7.7 +/- 6.5 atm 0 0.0% V: 60045 +/- 13 Ang^3 0 0.0% rho: 0.99646 +/- 0.00021 g/mL 0 0.0% Etotal: -75471 +/- 16 kJ/mol 0 0.0% a: 30 +/- 0 Ang 0 0.0% b: 30 +/- 0 Ang 0 0.0% c: 66.717 +/- 0.014 Ang 0 0.0% alpha: 90.00022 +/- 0 degree 0 0.0% beta: 90.00022 +/- 0 degree 0 0.0% gamma: 90.00022 +/- 0 degree 0 0.0% Epot: -90341 +/- 15 kJ/mol 0 0.0% Ekin: 14869.7 +/- 5.3 kJ/mol 0 0.0% Evdw: 21527 +/- 10 kJ/mol 0 0.0% Ecoul: -111868 +/- 20 kJ/mol 0 0.0% Sxx: -8 +/- 10 atm 0 0.0% Syy: -9.6 +/- 9.5 atm 0 0.0% Szz: -5.4 +/- 8.3 atm 0 0.0% Syz: 1.9 +/- 5.1 atm 0 0.0% Sxz: -1.5 +/- 6.3 atm 0 0.0% Sxy: -3.5 +/- 6.5 atm 0 0.0% LAMMPS stage successfully completed on 32 core(s) on Sun 06 August 2023 at 17:57:47 CST after 21627 s (6:00:27) Entire job completed on Sun 06 August 2023 at 17:57:47 CST after 21627 s (6:00:27) and running 1 tasks.