[Tue Aug 08 09:26:19 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir0/409/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/dir0/409/pcff+.frc) Current system formula: O2000H4000 (OH2) The nonbond terms are handled with a cutoff at 10 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/dir0/409/pcff+.frc) Current system formula: O2000H4000 (OH2) The nonbond terms are handled with a cutoff at 10 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: 5449.4 kJ/mol/Ang Fmax: 13.4 kJ/mol/Ang Initial Frms: 415.2 kJ/mol/Ang Frms: 0.6 kJ/mol/Ang P: -5229.9 atm V: 59830.2 Ang^3 rho: 1.0000 g/mL Sxx: 4877.4 atm Syy: 5510.1 atm Szz: 5302.2 atm Syz: 126.5 atm Sxz: -51.8 atm Sxy: -34.7 atm Initial Epot: 119895.8 kJ/mol Epot: -118405.5 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: 298.145 +/- 0.071 K 0 0.0% P: 90.8 +/- 8.4 atm 0 0.0% V: 59830.2 +/- 1.3e-09 Ang^3 0 0.0% rho: 1 +/- 0 g/mL 0 0.0% Etotal: -75542 +/- 18 kJ/mol 0 0.0% Epot: -90411 +/- 17 kJ/mol 0 0.0% Ekin: 14869.8 +/- 3.5 kJ/mol 0 0.0% Evdw: 21609 +/- 18 kJ/mol 0 0.0% Ecoul: -112020 +/- 32 kJ/mol 0 0.0% Sxx: -93 +/- 12 atm 0 0.0% Syy: -89 +/- 12 atm 0 0.0% Szz: -91 +/- 12 atm 0 0.0% Syz: 5.1 +/- 6.8 atm 0 0.0% Sxz: -2.4 +/- 6.2 atm 0 0.0% Sxy: 4.7 +/- 6.5 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: 298.239 +/- 0.056 K 0 0.0% P: 0.2 +/- 8.1 atm 0 0.0% V: 60052 +/- 20 Ang^3 0 0.0% rho: 0.99634 +/- 0.00033 g/mL 0 0.0% Etotal: -75474 +/- 13 kJ/mol 0 0.0% a: 30 +/- 0 Ang 0 0.0% b: 30 +/- 0 Ang 0 0.0% c: 66.724 +/- 0.022 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: -90348 +/- 12 kJ/mol 0 0.0% Ekin: 14874.5 +/- 2.8 kJ/mol 0 0.0% Evdw: 21525 +/- 13 kJ/mol 0 0.0% Ecoul: -111874 +/- 21 kJ/mol 0 0.0% Sxx: 6 +/- 12 atm 0 0.0% Syy: -3.7 +/- 9.3 atm 0 0.0% Szz: -2.5 +/- 6.9 atm 0 0.0% Syz: -0.4 +/- 6.3 atm 0 0.0% Sxz: 0.6 +/- 7.1 atm 0 0.0% Sxy: 0.6 +/- 4.9 atm 0 0.0% LAMMPS stage successfully completed on 32 core(s) on Tue 08 August 2023 at 15:53:58 CST after 23247 s (6:27:27) Entire job completed on Tue 08 August 2023 at 15:53:58 CST after 23247 s (6:27:27) and running 1 tasks.