Molecular dynamics (MD) simulates the time evolution of a molecular system by numerically integrating Newton’s equations of motion. At each timestep, forces acting on every atom are derived from the potential energy function of the underlying force field, and atomic positions and velocities are updated accordingly. By propagating the system over many timesteps, MD generates a trajectory from which thermodynamic quantities (temperature, pressure, free energy) and structural properties (radial distribution functions, conformational populations) can be extracted via statistical mechanics.
VeloxChem provides the OpenMMDynamics class as a high-level interface to run MD simulations with use of the OpenMM engine, see Gracia Trivino et al. (2025). Starting from a force field topology prepared with the MMForceFieldGenerator, a simulation can be set up and executed in a few lines of Python.
Creating solute force field¶
import veloxchem as vlx
molecule = vlx.Molecule.read_name("ethanol")
ff_gen = vlx.MMForceFieldGenerator()
ff_gen.create_topology(molecule)Reading ethanol from PubChem...
Reference: S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res., 2025, 53, D1516-D1525.
Please double-check the compound since names may refer to more than one record.
* Info * Using 6-31G* basis set for RESP charges...
* Info * Sum of partial charges is not a whole number.
* Info * Compensating by removing 1.000e-06 from the largest charge.
* Info * Using GAFF (v2.11) parameters.
Reference: J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case, J. Comput. Chem. 2004,
25, 1157-1174.
Running MD simulation¶
You can directly solvate your system by using the solvent option when you create a system. For more information about solvation, please visit the system solvation page.
opm_dyn = vlx.OpenMMDynamics()
opm_dyn.create_system_from_molecule(
molecule,
ff_gen,
filename="ethanol", # system parameters and coordinates written to .xml and .pdb
solvent="tip3p",
residue_name="ETH",
)
opm_dyn.run_md(
ensemble="NVT",
temperature=300, # in Kelvin
timestep=2.0, # in fs
nsteps=10000,
snapshots=200,
traj_file="ethanol_md.pdb",
) VeloxChem Solvation Builder
=============================
* Info * Solvating the solute with tip3p molecules
* Info * Padding: 1.0 nm
* Info * NPT Equilibration of the box requested
* Info * The box size is: 2.30 x 2.30 x 2.30 nm^3
* Info * The volume of the solute is: 0.06 nm^3
* Info * The volume available for the solvent is: 12.12 nm^3
* Info * The experimental density of tip3p is: 1000 kg/m^3
* Info * The solute is neutral, no counterions will be added
* Info * Solvated system with 403 solvent molecules out of 403 requested
* Info * Time to solvate the system: 0.24 s
* Info * The density of the solvent after packing is: 994 kg/m^3
* Info * The box size after equilibration is: 2.31 x 2.31 x 2.31 nm^3
* Info * The density of the solvent after equilibration is: 985 kg/m^3
* Info * Equilibrating the system
* Info * Duration: 10.0 ps
* Info * Temperature: 300 K
* Info * Pressure: 1 bar
* Info * Elapsed time to equilibrate the system: 1.68 s
* Info * Generating the ForceField for the solvent
* Info * solute.pdb, and solute.xml files written
* Info * solvent_1.xml file written
* Info * system.pdb file written
* Info * System parameters written to ethanol_system.xml
* Info * System coordinates written to ethanol_system.pdb
MD Simulation parameters:
==================================================
Ensemble: NVT
Temperature: 300 K
Friction: 1.0 1/ps
Timestep: 2.0 fs
Total simulation time in ns: 0.02
==================================================
Step: 0 / 10000 Time: 0.0 ps
Potential Energy -19980.136198212873 kJ/mol
Kinetic Energy: 3442.962890625 kJ/mol
Temperature: 291.4097503027307 K
Total Energy: -16537.173307587873 kJ/mol
------------------------------------------------------------
Step: 50 / 10000 Time: 0.1 ps
Potential Energy -18413.964638383142 kJ/mol
Kinetic Energy: 1947.6500244140625 kJ/mol
Temperature: 164.84761100302757 K
Total Energy: -16466.31461396908 kJ/mol
------------------------------------------------------------
Step: 100 / 10000 Time: 0.2 ps
Potential Energy -18315.166537472527 kJ/mol
Kinetic Energy: 1975.7476806640625 kJ/mol
Temperature: 167.22577517499693 K
Total Energy: -16339.418856808465 kJ/mol
------------------------------------------------------------
Step: 150 / 10000 Time: 0.3 ps
Potential Energy -18286.911042971085 kJ/mol
Kinetic Energy: 2244.23681640625 kJ/mol
Temperature: 189.9504906282686 K
Total Energy: -16042.674226564835 kJ/mol
------------------------------------------------------------
Step: 200 / 10000 Time: 0.4 ps
Potential Energy -18184.35652111798 kJ/mol
Kinetic Energy: 2440.1826171875 kJ/mol
Temperature: 206.53519359849645 K
Total Energy: -15744.173903930481 kJ/mol
------------------------------------------------------------
Step: 250 / 10000 Time: 0.5 ps
Potential Energy -17982.875385833453 kJ/mol
Kinetic Energy: 2484.2216796875 kJ/mol
Temperature: 210.26262622393543 K
Total Energy: -15498.653706145953 kJ/mol
------------------------------------------------------------
Step: 300 / 10000 Time: 0.6 ps
Potential Energy -17905.02816933907 kJ/mol
Kinetic Energy: 2569.822509765625 kJ/mol
Temperature: 217.50781512408201 K
Total Energy: -15335.205659573447 kJ/mol
------------------------------------------------------------
Step: 350 / 10000 Time: 0.7 ps
Potential Energy -17749.941117254566 kJ/mol
Kinetic Energy: 2622.21826171875 kJ/mol
Temperature: 221.9425515643613 K
Total Energy: -15127.722855535816 kJ/mol
------------------------------------------------------------
Step: 400 / 10000 Time: 0.8 ps
Potential Energy -17580.161041652333 kJ/mol
Kinetic Energy: 2653.77880859375 kJ/mol
Temperature: 224.61381215485574 K
Total Energy: -14926.382233058583 kJ/mol
------------------------------------------------------------
Step: 450 / 10000 Time: 0.9 ps
Potential Energy -17392.39158349998 kJ/mol
Kinetic Energy: 2685.22607421875 kJ/mol
Temperature: 227.27548470684232 K
Total Energy: -14707.165509281229 kJ/mol
------------------------------------------------------------
Step: 500 / 10000 Time: 1.0 ps
Potential Energy -17361.250314613353 kJ/mol
Kinetic Energy: 2808.16748046875 kJ/mol
Temperature: 237.68115146402178 K
Total Energy: -14553.082834144603 kJ/mol
------------------------------------------------------------
Step: 550 / 10000 Time: 1.1 ps
Potential Energy -17330.655529690455 kJ/mol
Kinetic Energy: 2914.08837890625 kJ/mol
Temperature: 246.6462154353937 K
Total Energy: -14416.567150784205 kJ/mol
------------------------------------------------------------
Step: 600 / 10000 Time: 1.2 ps
Potential Energy -17259.768863645862 kJ/mol
Kinetic Energy: 2944.131103515625 kJ/mol
Temperature: 249.18900870820835 K
Total Energy: -14315.637760130237 kJ/mol
------------------------------------------------------------
Step: 650 / 10000 Time: 1.3 ps
Potential Energy -17177.363540825914 kJ/mol
Kinetic Energy: 2968.60009765625 kJ/mol
Temperature: 251.26004568978445 K
Total Energy: -14208.763443169664 kJ/mol
------------------------------------------------------------
Step: 700 / 10000 Time: 1.4 ps
Potential Energy -17013.08624554194 kJ/mol
Kinetic Energy: 3060.77490234375 kJ/mol
Temperature: 259.06165078152895 K
Total Energy: -13952.311343198191 kJ/mol
------------------------------------------------------------
Step: 750 / 10000 Time: 1.5 ps
Potential Energy -17069.271487025093 kJ/mol
Kinetic Energy: 3143.92529296875 kJ/mol
Temperature: 266.0994363573145 K
Total Energy: -13925.346194056343 kJ/mol
------------------------------------------------------------
Step: 800 / 10000 Time: 1.6 ps
Potential Energy -16932.235285585295 kJ/mol
Kinetic Energy: 2989.6220703125 kJ/mol
Temperature: 253.03932940478163 K
Total Energy: -13942.613215272795 kJ/mol
------------------------------------------------------------
Step: 850 / 10000 Time: 1.7 ps
Potential Energy -16918.834537760835 kJ/mol
Kinetic Energy: 3055.17626953125 kJ/mol
Temperature: 258.58778677492876 K
Total Energy: -13863.658268229585 kJ/mol
------------------------------------------------------------
Step: 900 / 10000 Time: 1.8 ps
Potential Energy -16816.126714961152 kJ/mol
Kinetic Energy: 2997.0439453125 kJ/mol
Temperature: 253.66751123805585 K
Total Energy: -13819.082769648652 kJ/mol
------------------------------------------------------------
Step: 950 / 10000 Time: 1.9 ps
Potential Energy -16791.86443765975 kJ/mol
Kinetic Energy: 3114.56103515625 kJ/mol
Temperature: 263.6140679961667 K
Total Energy: -13677.303402503501 kJ/mol
------------------------------------------------------------
Step: 1000 / 10000 Time: 2.0 ps
Potential Energy -16694.567242173027 kJ/mol
Kinetic Energy: 3109.036865234375 kJ/mol
Temperature: 263.14650647177535 K
Total Energy: -13585.530376938652 kJ/mol
------------------------------------------------------------
Step: 1050 / 10000 Time: 2.1 ps
Potential Energy -16763.087834557067 kJ/mol
Kinetic Energy: 3108.92919921875 kJ/mol
Temperature: 263.1373937024176 K
Total Energy: -13654.158635338317 kJ/mol
------------------------------------------------------------
Step: 1100 / 10000 Time: 2.2 ps
Potential Energy -16745.710546945702 kJ/mol
Kinetic Energy: 3242.181640625 kJ/mol
Temperature: 274.4157786025743 K
Total Energy: -13503.528906320702 kJ/mol
------------------------------------------------------------
Step: 1150 / 10000 Time: 2.3 ps
Potential Energy -16821.871758078705 kJ/mol
Kinetic Energy: 3333.89599609375 kJ/mol
Temperature: 282.1784116240044 K
Total Energy: -13487.975761984955 kJ/mol
------------------------------------------------------------
Step: 1200 / 10000 Time: 2.4 ps
Potential Energy -16682.27448945075 kJ/mol
Kinetic Energy: 3291.285888671875 kJ/mol
Temperature: 278.57192466534684 K
Total Energy: -13390.988600778874 kJ/mol
------------------------------------------------------------
Step: 1250 / 10000 Time: 2.5 ps
Potential Energy -16608.695135352682 kJ/mol
Kinetic Energy: 3317.56103515625 kJ/mol
Temperature: 280.7958330022704 K
Total Energy: -13291.134100196432 kJ/mol
------------------------------------------------------------
Step: 1300 / 10000 Time: 2.6 ps
Potential Energy -16598.34364754289 kJ/mol
Kinetic Energy: 3371.51806640625 kJ/mol
Temperature: 285.36271493017426 K
Total Energy: -13226.82558113664 kJ/mol
------------------------------------------------------------
Step: 1350 / 10000 Time: 2.7 ps
Potential Energy -16487.300914573963 kJ/mol
Kinetic Energy: 3289.603515625 kJ/mol
Temperature: 278.4295298951793 K
Total Energy: -13197.697398948963 kJ/mol
------------------------------------------------------------
Step: 1400 / 10000 Time: 2.8 ps
Potential Energy -16510.15226462997 kJ/mol
Kinetic Energy: 3362.26025390625 kJ/mol
Temperature: 284.57914074866903 K
Total Energy: -13147.89201072372 kJ/mol
------------------------------------------------------------
Step: 1450 / 10000 Time: 2.9 ps
Potential Energy -16283.138960642289 kJ/mol
Kinetic Energy: 3072.18212890625 kJ/mol
Temperature: 260.02714972817057 K
Total Energy: -13210.956831736039 kJ/mol
------------------------------------------------------------
Step: 1500 / 10000 Time: 3.0 ps
Potential Energy -16435.150690389346 kJ/mol
Kinetic Energy: 3281.3994140625 kJ/mol
Temperature: 277.7351410028981 K
Total Energy: -13153.751276326846 kJ/mol
------------------------------------------------------------
Step: 1550 / 10000 Time: 3.1 ps
Potential Energy -16483.563512725304 kJ/mol
Kinetic Energy: 3298.395263671875 kJ/mol
Temperature: 279.17365673722 K
Total Energy: -13185.16824905343 kJ/mol
------------------------------------------------------------
Step: 1600 / 10000 Time: 3.2 ps
Potential Energy -16500.65109518684 kJ/mol
Kinetic Energy: 3344.581298828125 kJ/mol
Temperature: 283.0828074890345 K
Total Energy: -13156.069796358715 kJ/mol
------------------------------------------------------------
Step: 1650 / 10000 Time: 3.3 ps
Potential Energy -16326.715913956534 kJ/mol
Kinetic Energy: 3339.94970703125 kJ/mol
Temperature: 282.69079309564484 K
Total Energy: -12986.766206925284 kJ/mol
------------------------------------------------------------
Step: 1700 / 10000 Time: 3.4 ps
Potential Energy -16297.395604116391 kJ/mol
Kinetic Energy: 3411.962890625 kJ/mol
Temperature: 288.78593397174933 K
Total Energy: -12885.432713491391 kJ/mol
------------------------------------------------------------
Step: 1750 / 10000 Time: 3.5 ps
Potential Energy -16224.499185999404 kJ/mol
Kinetic Energy: 3436.152587890625 kJ/mol
Temperature: 290.8333314790733 K
Total Energy: -12788.34659810878 kJ/mol
------------------------------------------------------------
Step: 1800 / 10000 Time: 3.6 ps
Potential Energy -16391.757590991925 kJ/mol
Kinetic Energy: 3545.47265625 kJ/mol
Temperature: 300.0860985973096 K
Total Energy: -12846.284934741925 kJ/mol
------------------------------------------------------------
Step: 1850 / 10000 Time: 3.7 ps
Potential Energy -16413.610747074257 kJ/mol
Kinetic Energy: 3553.946533203125 kJ/mol
Temperature: 300.8033210726753 K
Total Energy: -12859.664213871132 kJ/mol
------------------------------------------------------------
Step: 1900 / 10000 Time: 3.8 ps
Potential Energy -16209.545870398651 kJ/mol
Kinetic Energy: 3293.3095703125 kJ/mol
Temperature: 278.7432075342945 K
Total Energy: -12916.236300086151 kJ/mol
------------------------------------------------------------
Step: 1950 / 10000 Time: 3.9 ps
Potential Energy -16362.248593290817 kJ/mol
Kinetic Energy: 3511.1533203125 kJ/mol
Temperature: 297.1813362069468 K
Total Energy: -12851.095272978317 kJ/mol
------------------------------------------------------------
Step: 2000 / 10000 Time: 4.0 ps
Potential Energy -16228.474872266423 kJ/mol
Kinetic Energy: 3390.550048828125 kJ/mol
Temperature: 286.97356739112485 K
Total Energy: -12837.924823438298 kJ/mol
------------------------------------------------------------
Step: 2050 / 10000 Time: 4.1 ps
Potential Energy -16298.49723429374 kJ/mol
Kinetic Energy: 3411.01806640625 kJ/mol
Temperature: 288.7059647712635 K
Total Energy: -12887.47916788749 kJ/mol
------------------------------------------------------------
Step: 2100 / 10000 Time: 4.2 ps
Potential Energy -16260.447460753392 kJ/mol
Kinetic Energy: 3444.65869140625 kJ/mol
Temperature: 291.5532815860835 K
Total Energy: -12815.788769347142 kJ/mol
------------------------------------------------------------
Step: 2150 / 10000 Time: 4.3 ps
Potential Energy -16325.917431925904 kJ/mol
Kinetic Energy: 3471.595703125 kJ/mol
Temperature: 293.83320969109934 K
Total Energy: -12854.321728800904 kJ/mol
------------------------------------------------------------
Step: 2200 / 10000 Time: 4.4 ps
Potential Energy -16323.082894889187 kJ/mol
Kinetic Energy: 3370.652587890625 kJ/mol
Temperature: 285.2894614894191 K
Total Energy: -12952.430306998562 kJ/mol
------------------------------------------------------------
Step: 2250 / 10000 Time: 4.5 ps
Potential Energy -16237.369251509677 kJ/mol
Kinetic Energy: 3377.98681640625 kJ/mol
Temperature: 285.9102249911755 K
Total Energy: -12859.382435103427 kJ/mol
------------------------------------------------------------
Step: 2300 / 10000 Time: 4.6 ps
Potential Energy -16142.780113616507 kJ/mol
Kinetic Energy: 3272.35400390625 kJ/mol
Temperature: 276.96954439359513 K
Total Energy: -12870.426109710257 kJ/mol
------------------------------------------------------------
Step: 2350 / 10000 Time: 4.7 ps
Potential Energy -16112.373749428909 kJ/mol
Kinetic Energy: 3340.6357421875 kJ/mol
Temperature: 282.7488585874705 K
Total Energy: -12771.738007241409 kJ/mol
------------------------------------------------------------
Step: 2400 / 10000 Time: 4.8 ps
Potential Energy -16129.823788446854 kJ/mol
Kinetic Energy: 3436.505859375 kJ/mol
Temperature: 290.8632321077821 K
Total Energy: -12693.317929071854 kJ/mol
------------------------------------------------------------
Step: 2450 / 10000 Time: 4.9 ps
Potential Energy -16171.508655456375 kJ/mol
Kinetic Energy: 3446.7431640625 kJ/mol
Temperature: 291.7297097601787 K
Total Energy: -12724.765491393875 kJ/mol
------------------------------------------------------------
Step: 2500 / 10000 Time: 5.0 ps
Potential Energy -16087.941299734186 kJ/mol
Kinetic Energy: 3461.87841796875 kJ/mol
Temperature: 293.0107460947841 K
Total Energy: -12626.062881765436 kJ/mol
------------------------------------------------------------
Step: 2550 / 10000 Time: 5.1 ps
Potential Energy -16082.70388653643 kJ/mol
Kinetic Energy: 3538.421630859375 kJ/mol
Temperature: 299.489305191823 K
Total Energy: -12544.282255677055 kJ/mol
------------------------------------------------------------
Step: 2600 / 10000 Time: 5.2 ps
Potential Energy -16073.826524471413 kJ/mol
Kinetic Energy: 3578.953857421875 kJ/mol
Temperature: 302.9199219010399 K
Total Energy: -12494.872667049538 kJ/mol
------------------------------------------------------------
Step: 2650 / 10000 Time: 5.3 ps
Potential Energy -16030.686221317868 kJ/mol
Kinetic Energy: 3462.443359375 kJ/mol
Temperature: 293.0585623040669 K
Total Energy: -12568.242861942868 kJ/mol
------------------------------------------------------------
Step: 2700 / 10000 Time: 5.4 ps
Potential Energy -16053.903847408961 kJ/mol
Kinetic Energy: 3465.3603515625 kJ/mol
Temperature: 293.3054542956446 K
Total Energy: -12588.543495846461 kJ/mol
------------------------------------------------------------
Step: 2750 / 10000 Time: 5.5 ps
Potential Energy -16129.70608315758 kJ/mol
Kinetic Energy: 3447.49853515625 kJ/mol
Temperature: 291.79364379281526 K
Total Energy: -12682.20754800133 kJ/mol
------------------------------------------------------------
Step: 2800 / 10000 Time: 5.6 ps
Potential Energy -16134.318566655289 kJ/mol
Kinetic Energy: 3526.87109375 kJ/mol
Temperature: 298.5116765499138 K
Total Energy: -12607.447472905289 kJ/mol
------------------------------------------------------------
Step: 2850 / 10000 Time: 5.7 ps
Potential Energy -15987.544158739518 kJ/mol
Kinetic Energy: 3382.6826171875 kJ/mol
Temperature: 286.307673983978 K
Total Energy: -12604.861541552018 kJ/mol
------------------------------------------------------------
Step: 2900 / 10000 Time: 5.8 ps
Potential Energy -15998.260689807605 kJ/mol
Kinetic Energy: 3460.16748046875 kJ/mol
Temperature: 292.8659336511135 K
Total Energy: -12538.093209338855 kJ/mol
------------------------------------------------------------
Step: 2950 / 10000 Time: 5.9 ps
Potential Energy -16006.74184401102 kJ/mol
Kinetic Energy: 3494.43359375 kJ/mol
Temperature: 295.7661913164877 K
Total Energy: -12512.30825026102 kJ/mol
------------------------------------------------------------
Step: 3000 / 10000 Time: 6.0 ps
Potential Energy -15958.468528521727 kJ/mol
Kinetic Energy: 3442.55224609375 kJ/mol
Temperature: 291.37499366313966 K
Total Energy: -12515.916282427977 kJ/mol
------------------------------------------------------------
Step: 3050 / 10000 Time: 6.1 ps
Potential Energy -16047.506160405945 kJ/mol
Kinetic Energy: 3494.406982421875 kJ/mol
Temperature: 295.76393895399343 K
Total Energy: -12553.09917798407 kJ/mol
------------------------------------------------------------
Step: 3100 / 10000 Time: 6.2 ps
Potential Energy -15953.946589795421 kJ/mol
Kinetic Energy: 3456.538330078125 kJ/mol
Temperature: 292.55876513296806 K
Total Energy: -12497.408259717296 kJ/mol
------------------------------------------------------------
Step: 3150 / 10000 Time: 6.3 ps
Potential Energy -15976.629854311715 kJ/mol
Kinetic Energy: 3433.677734375 kJ/mol
Temperature: 290.6238617671029 K
Total Energy: -12542.952119936715 kJ/mol
------------------------------------------------------------
Step: 3200 / 10000 Time: 6.4 ps
Potential Energy -15931.345256825458 kJ/mol
Kinetic Energy: 3422.87548828125 kJ/mol
Temperature: 289.70956790542346 K
Total Energy: -12508.469768544208 kJ/mol
------------------------------------------------------------
Step: 3250 / 10000 Time: 6.5 ps
Potential Energy -16079.606114035021 kJ/mol
Kinetic Energy: 3578.392822265625 kJ/mol
Temperature: 302.8724363137746 K
Total Energy: -12501.213291769396 kJ/mol
------------------------------------------------------------
Step: 3300 / 10000 Time: 6.6 ps
Potential Energy -16026.418738958906 kJ/mol
Kinetic Energy: 3535.591064453125 kJ/mol
Temperature: 299.24972821238276 K
Total Energy: -12490.827674505781 kJ/mol
------------------------------------------------------------
Step: 3350 / 10000 Time: 6.7 ps
Potential Energy -15915.857827974032 kJ/mol
Kinetic Energy: 3523.58056640625 kJ/mol
Temperature: 298.2331688279115 K
Total Energy: -12392.277261567782 kJ/mol
------------------------------------------------------------
Step: 3400 / 10000 Time: 6.8 ps
Potential Energy -15896.46355975933 kJ/mol
Kinetic Energy: 3543.99072265625 kJ/mol
Temperature: 299.96066886941577 K
Total Energy: -12352.47283710308 kJ/mol
------------------------------------------------------------
Step: 3450 / 10000 Time: 6.9 ps
Potential Energy -15983.326414165567 kJ/mol
Kinetic Energy: 3667.27490234375 kJ/mol
Temperature: 310.3953477086319 K
Total Energy: -12316.051511821817 kJ/mol
------------------------------------------------------------
Step: 3500 / 10000 Time: 7.0 ps
Potential Energy -15977.209337679218 kJ/mol
Kinetic Energy: 3553.1044921875 kJ/mol
Temperature: 300.7320513640252 K
Total Energy: -12424.104845491718 kJ/mol
------------------------------------------------------------
Step: 3550 / 10000 Time: 7.1 ps
Potential Energy -15984.811742176782 kJ/mol
Kinetic Energy: 3574.07373046875 kJ/mol
Temperature: 302.506871681786 K
Total Energy: -12410.738011708032 kJ/mol
------------------------------------------------------------
Step: 3600 / 10000 Time: 7.2 ps
Potential Energy -15802.552695845734 kJ/mol
Kinetic Energy: 3480.919921875 kJ/mol
Temperature: 294.6224044469023 K
Total Energy: -12321.632773970734 kJ/mol
------------------------------------------------------------
Step: 3650 / 10000 Time: 7.3 ps
Potential Energy -15840.75280195057 kJ/mol
Kinetic Energy: 3666.390380859375 kJ/mol
Temperature: 310.3204824855414 K
Total Energy: -12174.362421091195 kJ/mol
------------------------------------------------------------
Step: 3700 / 10000 Time: 7.4 ps
Potential Energy -15758.047120173942 kJ/mol
Kinetic Energy: 3579.29052734375 kJ/mol
Temperature: 302.9484173861743 K
Total Energy: -12178.756592830192 kJ/mol
------------------------------------------------------------
Step: 3750 / 10000 Time: 7.5 ps
Potential Energy -15857.80991659082 kJ/mol
Kinetic Energy: 3657.99560546875 kJ/mol
Temperature: 309.6099551060303 K
Total Energy: -12199.81431112207 kJ/mol
------------------------------------------------------------
Step: 3800 / 10000 Time: 7.6 ps
Potential Energy -15874.211820272278 kJ/mol
Kinetic Energy: 3692.126953125 kJ/mol
Temperature: 312.49880631180037 K
Total Energy: -12182.084867147278 kJ/mol
------------------------------------------------------------
Step: 3850 / 10000 Time: 7.7 ps
Potential Energy -15874.87405363984 kJ/mol
Kinetic Energy: 3635.806640625 kJ/mol
Temperature: 307.73189806330123 K
Total Energy: -12239.06741301484 kJ/mol
------------------------------------------------------------
Step: 3900 / 10000 Time: 7.8 ps
Potential Energy -15891.018076864551 kJ/mol
Kinetic Energy: 3640.652587890625 kJ/mol
Temperature: 308.1420553399019 K
Total Energy: -12250.365488973926 kJ/mol
------------------------------------------------------------
Step: 3950 / 10000 Time: 7.9 ps
Potential Energy -15969.77442718811 kJ/mol
Kinetic Energy: 3697.51025390625 kJ/mol
Temperature: 312.95444477968516 K
Total Energy: -12272.26417328186 kJ/mol
------------------------------------------------------------
Step: 4000 / 10000 Time: 8.0 ps
Potential Energy -15683.395992667894 kJ/mol
Kinetic Energy: 3479.00537109375 kJ/mol
Temperature: 294.4603583305689 K
Total Energy: -12204.390621574144 kJ/mol
------------------------------------------------------------
Step: 4050 / 10000 Time: 8.1 ps
Potential Energy -15801.64362236626 kJ/mol
Kinetic Energy: 3558.07080078125 kJ/mol
Temperature: 301.1523959315405 K
Total Energy: -12243.57282158501 kJ/mol
------------------------------------------------------------
Step: 4100 / 10000 Time: 8.2 ps
Potential Energy -15852.478236211013 kJ/mol
Kinetic Energy: 3615.487060546875 kJ/mol
Temperature: 306.0120643198281 K
Total Energy: -12236.991175664138 kJ/mol
------------------------------------------------------------
Step: 4150 / 10000 Time: 8.3 ps
Potential Energy -15891.277247307371 kJ/mol
Kinetic Energy: 3547.29248046875 kJ/mol
Temperature: 300.24012712971836 K
Total Energy: -12343.984766838621 kJ/mol
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Step: 4200 / 10000 Time: 8.4 ps
Potential Energy -15984.512084712755 kJ/mol
Kinetic Energy: 3621.123046875 kJ/mol
Temperature: 306.4890898994707 K
Total Energy: -12363.389037837755 kJ/mol
------------------------------------------------------------
Step: 4250 / 10000 Time: 8.5 ps
Potential Energy -15971.991898586522 kJ/mol
Kinetic Energy: 3632.195068359375 kJ/mol
Temperature: 307.4262173442346 K
Total Energy: -12339.796830227147 kJ/mol
------------------------------------------------------------
Step: 4300 / 10000 Time: 8.6 ps
Potential Energy -15984.086026694175 kJ/mol
Kinetic Energy: 3584.357421875 kJ/mol
Temperature: 303.37727547064054 K
Total Energy: -12399.728604819175 kJ/mol
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Step: 4350 / 10000 Time: 8.7 ps
Potential Energy -15950.989306253861 kJ/mol
Kinetic Energy: 3500.810302734375 kJ/mol
Temperature: 296.30591109620127 K
Total Energy: -12450.179003519486 kJ/mol
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Step: 4400 / 10000 Time: 8.8 ps
Potential Energy -15907.476416904028 kJ/mol
Kinetic Energy: 3453.21142578125 kJ/mol
Temperature: 292.27717849342764 K
Total Energy: -12454.264991122778 kJ/mol
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Step: 4450 / 10000 Time: 8.9 ps
Potential Energy -16042.488314194154 kJ/mol
Kinetic Energy: 3624.211669921875 kJ/mol
Temperature: 306.75050859594285 K
Total Energy: -12418.276644272279 kJ/mol
------------------------------------------------------------
Step: 4500 / 10000 Time: 9.0 ps
Potential Energy -16086.268835430514 kJ/mol
Kinetic Energy: 3585.45458984375 kJ/mol
Temperature: 303.4701389298094 K
Total Energy: -12500.814245586764 kJ/mol
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Step: 4550 / 10000 Time: 9.1 ps
Potential Energy -15882.380065811347 kJ/mol
Kinetic Energy: 3417.30029296875 kJ/mol
Temperature: 289.2376876309284 K
Total Energy: -12465.079772842597 kJ/mol
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Step: 4600 / 10000 Time: 9.2 ps
Potential Energy -16000.26563807718 kJ/mol
Kinetic Energy: 3597.42578125 kJ/mol
Temperature: 304.4833714302295 K
Total Energy: -12402.83985682718 kJ/mol
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Step: 4650 / 10000 Time: 9.3 ps
Potential Energy -15867.009984632503 kJ/mol
Kinetic Energy: 3550.62646484375 kJ/mol
Temperature: 300.5223130216655 K
Total Energy: -12316.383519788753 kJ/mol
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Step: 4700 / 10000 Time: 9.4 ps
Potential Energy -15935.897097764086 kJ/mol
Kinetic Energy: 3721.39306640625 kJ/mol
Temperature: 314.97586779475824 K
Total Energy: -12214.504031357836 kJ/mol
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Step: 4750 / 10000 Time: 9.5 ps
Potential Energy -15982.465067374069 kJ/mol
Kinetic Energy: 3779.81884765625 kJ/mol
Temperature: 319.9209813106968 K
Total Energy: -12202.646219717819 kJ/mol
------------------------------------------------------------
Step: 4800 / 10000 Time: 9.6 ps
Potential Energy -15959.717450568001 kJ/mol
Kinetic Energy: 3667.46875 kJ/mol
Temperature: 310.411754826251 K
Total Energy: -12292.248700568001 kJ/mol
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Step: 4850 / 10000 Time: 9.7 ps
Potential Energy -15984.779118664112 kJ/mol
Kinetic Energy: 3671.0654296875 kJ/mol
Temperature: 310.71617504887587 K
Total Energy: -12313.713688976612 kJ/mol
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Step: 4900 / 10000 Time: 9.8 ps
Potential Energy -15914.882461728077 kJ/mol
Kinetic Energy: 3487.543701171875 kJ/mol
Temperature: 295.18303606922353 K
Total Energy: -12427.338760556202 kJ/mol
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Step: 4950 / 10000 Time: 9.9 ps
Potential Energy -15874.977430847954 kJ/mol
Kinetic Energy: 3529.36669921875 kJ/mol
Temperature: 298.72290269135226 K
Total Energy: -12345.610731629204 kJ/mol
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Step: 5000 / 10000 Time: 10.0 ps
Potential Energy -15986.620890380364 kJ/mol
Kinetic Energy: 3569.97509765625 kJ/mol
Temperature: 302.15996652991066 K
Total Energy: -12416.645792724114 kJ/mol
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Step: 5050 / 10000 Time: 10.1 ps
Potential Energy -15986.689055708717 kJ/mol
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Temperature: 299.80050316580684 K
Total Energy: -12444.590667036842 kJ/mol
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Step: 5100 / 10000 Time: 10.2 ps
Potential Energy -16022.837476668428 kJ/mol
Kinetic Energy: 3514.625244140625 kJ/mol
Temperature: 297.47519718888736 K
Total Energy: -12508.212232527803 kJ/mol
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Step: 5150 / 10000 Time: 10.3 ps
Potential Energy -16085.781704475652 kJ/mol
Kinetic Energy: 3664.757568359375 kJ/mol
Temperature: 310.18228248222107 K
Total Energy: -12421.024136116277 kJ/mol
------------------------------------------------------------
Step: 5200 / 10000 Time: 10.4 ps
Potential Energy -16061.25224472351 kJ/mol
Kinetic Energy: 3565.889892578125 kJ/mol
Temperature: 301.8141978912206 K
Total Energy: -12495.362352145385 kJ/mol
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Step: 5250 / 10000 Time: 10.5 ps
Potential Energy -15974.881651440184 kJ/mol
Kinetic Energy: 3482.41455078125 kJ/mol
Temperature: 294.74890869635317 K
Total Energy: -12492.467100658934 kJ/mol
------------------------------------------------------------
Step: 5300 / 10000 Time: 10.6 ps
Potential Energy -15909.599781354438 kJ/mol
Kinetic Energy: 3486.984130859375 kJ/mol
Temperature: 295.13567446521483 K
Total Energy: -12422.615650495063 kJ/mol
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Step: 5350 / 10000 Time: 10.7 ps
Potential Energy -16034.79231419928 kJ/mol
Kinetic Energy: 3519.468017578125 kJ/mol
Temperature: 297.88508583509883 K
Total Energy: -12515.324296621155 kJ/mol
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Step: 5400 / 10000 Time: 10.8 ps
Potential Energy -16049.16117289431 kJ/mol
Kinetic Energy: 3472.591552734375 kJ/mol
Temperature: 293.917497641689 K
Total Energy: -12576.569620159935 kJ/mol
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Step: 5450 / 10000 Time: 10.9 ps
Potential Energy -16077.304215801429 kJ/mol
Kinetic Energy: 3491.65478515625 kJ/mol
Temperature: 295.5309950787796 K
Total Energy: -12585.649430645179 kJ/mol
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Step: 5500 / 10000 Time: 11.0 ps
Potential Energy -15974.660607050653 kJ/mol
Kinetic Energy: 3343.029296875 kJ/mol
Temperature: 282.95144722870145 K
Total Energy: -12631.631310175653 kJ/mol
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Step: 5550 / 10000 Time: 11.1 ps
Potential Energy -16051.421645415496 kJ/mol
Kinetic Energy: 3497.874755859375 kJ/mol
Temperature: 296.0574486500404 K
Total Energy: -12553.54688955612 kJ/mol
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Step: 5600 / 10000 Time: 11.2 ps
Potential Energy -16147.530996879112 kJ/mol
Kinetic Energy: 3501.95947265625 kJ/mol
Temperature: 296.40317596097833 K
Total Energy: -12645.571524222862 kJ/mol
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Step: 5650 / 10000 Time: 11.3 ps
Potential Energy -16117.489799377989 kJ/mol
Kinetic Energy: 3427.86767578125 kJ/mol
Temperature: 290.13210284380483 K
Total Energy: -12689.622123596739 kJ/mol
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Step: 5700 / 10000 Time: 11.4 ps
Potential Energy -16053.349628997516 kJ/mol
Kinetic Energy: 3418.149658203125 kJ/mol
Temperature: 289.3095772558613 K
Total Energy: -12635.19997079439 kJ/mol
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Step: 5750 / 10000 Time: 11.5 ps
Potential Energy -15992.856621978353 kJ/mol
Kinetic Energy: 3370.443359375 kJ/mol
Temperature: 285.2717525476061 K
Total Energy: -12622.413262603353 kJ/mol
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Step: 5800 / 10000 Time: 11.6 ps
Potential Energy -16114.71895330913 kJ/mol
Kinetic Energy: 3501.97021484375 kJ/mol
Temperature: 296.40408517152645 K
Total Energy: -12612.74873846538 kJ/mol
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Step: 5850 / 10000 Time: 11.7 ps
Potential Energy -16047.15907783575 kJ/mol
Kinetic Energy: 3412.006591796875 kJ/mol
Temperature: 288.7896328055703 K
Total Energy: -12635.152486038874 kJ/mol
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Step: 5900 / 10000 Time: 11.8 ps
Potential Energy -16167.950620108764 kJ/mol
Kinetic Energy: 3525.9638671875 kJ/mol
Temperature: 298.43488958634646 K
Total Energy: -12641.986752921264 kJ/mol
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Step: 5950 / 10000 Time: 11.9 ps
Potential Energy -16316.327214655947 kJ/mol
Kinetic Energy: 3642.06640625 kJ/mol
Temperature: 308.26171984636545 K
Total Energy: -12674.260808405947 kJ/mol
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Step: 6000 / 10000 Time: 12.0 ps
Potential Energy -16311.389235985946 kJ/mol
Kinetic Energy: 3608.4541015625 kJ/mol
Temperature: 305.41680004117245 K
Total Energy: -12702.935134423446 kJ/mol
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Step: 6050 / 10000 Time: 12.1 ps
Potential Energy -16211.903432113599 kJ/mol
Kinetic Energy: 3488.411865234375 kJ/mol
Temperature: 295.2565168126157 K
Total Energy: -12723.491566879224 kJ/mol
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Step: 6100 / 10000 Time: 12.2 ps
Potential Energy -16052.929297914277 kJ/mol
Kinetic Energy: 3385.21728515625 kJ/mol
Temperature: 286.5222063455916 K
Total Energy: -12667.712012758027 kJ/mol
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Step: 6150 / 10000 Time: 12.3 ps
Potential Energy -16181.875418984811 kJ/mol
Kinetic Energy: 3426.27685546875 kJ/mol
Temperature: 289.99745702717274 K
Total Energy: -12755.598563516061 kJ/mol
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Step: 6200 / 10000 Time: 12.4 ps
Potential Energy -16190.838388917517 kJ/mol
Kinetic Energy: 3541.271484375 kJ/mol
Temperature: 299.7305146174746 K
Total Energy: -12649.566904542517 kJ/mol
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Step: 6250 / 10000 Time: 12.5 ps
Potential Energy -16169.071373847793 kJ/mol
Kinetic Energy: 3467.86962890625 kJ/mol
Temperature: 293.51783761414436 K
Total Energy: -12701.201744941543 kJ/mol
------------------------------------------------------------
Step: 6300 / 10000 Time: 12.6 ps
Potential Energy -16279.670496029328 kJ/mol
Kinetic Energy: 3594.7841796875 kJ/mol
Temperature: 304.25978829088643 K
Total Energy: -12684.886316341828 kJ/mol
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Step: 6350 / 10000 Time: 12.7 ps
Potential Energy -16141.251385030817 kJ/mol
Kinetic Energy: 3427.185791015625 kJ/mol
Temperature: 290.07438863787274 K
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Step: 6400 / 10000 Time: 12.8 ps
Potential Energy -16170.60317971326 kJ/mol
Kinetic Energy: 3456.98681640625 kJ/mol
Temperature: 292.5967246733537 K
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Step: 6450 / 10000 Time: 12.9 ps
Potential Energy -16084.15390077747 kJ/mol
Kinetic Energy: 3520.51171875 kJ/mol
Temperature: 297.973423905403 K
Total Energy: -12563.64218202747 kJ/mol
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Step: 6500 / 10000 Time: 13.0 ps
Potential Energy -16203.850350779961 kJ/mol
Kinetic Energy: 3558.8134765625 kJ/mol
Temperature: 301.2152554426201 K
Total Energy: -12645.036874217461 kJ/mol
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Step: 6550 / 10000 Time: 13.1 ps
Potential Energy -16151.903358695577 kJ/mol
Kinetic Energy: 3500.7568359375 kJ/mol
Temperature: 296.3013857073366 K
Total Energy: -12651.146522758077 kJ/mol
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Step: 6600 / 10000 Time: 13.2 ps
Potential Energy -15865.023797532092 kJ/mol
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Temperature: 275.42828786733105 K
Total Energy: -12610.879510422717 kJ/mol
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Step: 6650 / 10000 Time: 13.3 ps
Potential Energy -15979.739415080767 kJ/mol
Kinetic Energy: 3396.17529296875 kJ/mol
Temperature: 287.4496837602193 K
Total Energy: -12583.564122112017 kJ/mol
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Step: 6700 / 10000 Time: 13.4 ps
Potential Energy -16074.501420793604 kJ/mol
Kinetic Energy: 3503.975830078125 kJ/mol
Temperature: 296.5738389136432 K
Total Energy: -12570.525590715479 kJ/mol
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Step: 6750 / 10000 Time: 13.5 ps
Potential Energy -15986.026863691877 kJ/mol
Kinetic Energy: 3470.2041015625 kJ/mol
Temperature: 293.7154255973604 K
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Step: 6800 / 10000 Time: 13.6 ps
Potential Energy -15974.738852513503 kJ/mol
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Temperature: 283.686337318128 K
Total Energy: -12623.026938451003 kJ/mol
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Step: 6850 / 10000 Time: 13.7 ps
Potential Energy -16095.82673887677 kJ/mol
Kinetic Energy: 3499.6953125 kJ/mol
Temperature: 296.2115391740774 K
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Step: 6900 / 10000 Time: 13.8 ps
Potential Energy -16162.447885503541 kJ/mol
Kinetic Energy: 3648.20654296875 kJ/mol
Temperature: 308.7814163301433 K
Total Energy: -12514.241342534791 kJ/mol
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Step: 6950 / 10000 Time: 13.9 ps
Potential Energy -15999.07638789482 kJ/mol
Kinetic Energy: 3515.080078125 kJ/mol
Temperature: 297.51369399005154 K
Total Energy: -12483.99630976982 kJ/mol
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Step: 7000 / 10000 Time: 14.0 ps
Potential Energy -15939.944860053729 kJ/mol
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Temperature: 292.7128556570051 K
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Step: 7050 / 10000 Time: 14.1 ps
Potential Energy -15962.650270664613 kJ/mol
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Temperature: 291.7817414001848 K
Total Energy: -12515.292360508363 kJ/mol
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Step: 7100 / 10000 Time: 14.2 ps
Potential Energy -16041.494323057603 kJ/mol
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Temperature: 297.75172117878463 K
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Step: 7150 / 10000 Time: 14.3 ps
Potential Energy -16091.047616702985 kJ/mol
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Temperature: 295.9779753825808 K
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Step: 7200 / 10000 Time: 14.4 ps
Potential Energy -16015.541211226504 kJ/mol
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Temperature: 290.82756625764296 K
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Step: 7250 / 10000 Time: 14.5 ps
Potential Energy -16110.394765952151 kJ/mol
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Temperature: 297.69648663798387 K
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Step: 7300 / 10000 Time: 14.6 ps
Potential Energy -15989.517967948239 kJ/mol
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Temperature: 285.2945034751862 K
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Step: 7350 / 10000 Time: 14.7 ps
Potential Energy -16136.334988986622 kJ/mol
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Temperature: 302.6151503925214 K
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Step: 7400 / 10000 Time: 14.8 ps
Potential Energy -16109.876606674414 kJ/mol
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Temperature: 294.99166791271193 K
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Step: 7450 / 10000 Time: 14.9 ps
Potential Energy -16224.646949676346 kJ/mol
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Temperature: 300.6657203217617 K
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Step: 7500 / 10000 Time: 15.0 ps
Potential Energy -16213.232545358609 kJ/mol
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Temperature: 299.50866724372355 K
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Step: 7550 / 10000 Time: 15.1 ps
Potential Energy -16126.437025343548 kJ/mol
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Temperature: 288.95926256443045 K
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Step: 7600 / 10000 Time: 15.2 ps
Potential Energy -16101.966074598502 kJ/mol
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Temperature: 283.72115594934735 K
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Step: 7650 / 10000 Time: 15.3 ps
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Temperature: 273.14815312355415 K
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Step: 7700 / 10000 Time: 15.4 ps
Potential Energy -16010.704140705537 kJ/mol
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Temperature: 291.437357241193 K
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Step: 7750 / 10000 Time: 15.5 ps
Potential Energy -15973.133907665979 kJ/mol
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Temperature: 291.53484940860716 K
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Step: 7800 / 10000 Time: 15.6 ps
Potential Energy -15810.551238486092 kJ/mol
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Temperature: 288.8235008984892 K
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Step: 7850 / 10000 Time: 15.7 ps
Potential Energy -15897.008045276176 kJ/mol
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Temperature: 298.38455238418015 K
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Step: 7900 / 10000 Time: 15.8 ps
Potential Energy -15971.651943621706 kJ/mol
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Temperature: 306.95551491067687 K
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Step: 7950 / 10000 Time: 15.9 ps
Potential Energy -16010.458838363658 kJ/mol
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Temperature: 307.2111683857186 K
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Step: 8000 / 10000 Time: 16.0 ps
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Temperature: 306.50582763910734 K
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Step: 8050 / 10000 Time: 16.1 ps
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Temperature: 306.35560125989997 K
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Step: 8100 / 10000 Time: 16.2 ps
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Temperature: 307.76708864429025 K
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Step: 8150 / 10000 Time: 16.3 ps
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Temperature: 309.360066852419 K
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Step: 8200 / 10000 Time: 16.4 ps
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Temperature: 303.66966931737835 K
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Step: 8250 / 10000 Time: 16.5 ps
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Temperature: 297.12155561340523 K
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Step: 8300 / 10000 Time: 16.6 ps
Potential Energy -15799.44272574551 kJ/mol
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Temperature: 310.16637129762825 K
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Step: 8350 / 10000 Time: 16.7 ps
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Temperature: 326.4925278501611 K
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Step: 8400 / 10000 Time: 16.8 ps
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Temperature: 326.26003858022136 K
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Step: 8450 / 10000 Time: 16.9 ps
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Temperature: 305.82009691090974 K
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Step: 8500 / 10000 Time: 17.0 ps
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Temperature: 312.99337552224733 K
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Step: 8550 / 10000 Time: 17.1 ps
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Temperature: 308.37047382625104 K
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Step: 8600 / 10000 Time: 17.2 ps
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Temperature: 307.3772026301383 K
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Step: 8650 / 10000 Time: 17.3 ps
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Temperature: 304.8354218872523 K
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Step: 8700 / 10000 Time: 17.4 ps
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Temperature: 307.6084933952646 K
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Step: 8750 / 10000 Time: 17.5 ps
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Temperature: 311.49185562971303 K
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Step: 8800 / 10000 Time: 17.6 ps
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Temperature: 313.3511292090722 K
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Step: 8850 / 10000 Time: 17.7 ps
Potential Energy -15805.293148723911 kJ/mol
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Temperature: 297.09095241290925 K
Total Energy: -12295.207699505161 kJ/mol
------------------------------------------------------------
Step: 8900 / 10000 Time: 17.8 ps
Potential Energy -15823.22725973792 kJ/mol
Kinetic Energy: 3543.04345703125 kJ/mol
Temperature: 299.8804930301689 K
Total Energy: -12280.18380270667 kJ/mol
------------------------------------------------------------
Step: 8950 / 10000 Time: 17.9 ps
Potential Energy -15690.252402739148 kJ/mol
Kinetic Energy: 3390.150146484375 kJ/mol
Temperature: 286.93971996208194 K
Total Energy: -12300.102256254773 kJ/mol
------------------------------------------------------------
Step: 9000 / 10000 Time: 18.0 ps
Potential Energy -15808.392467600774 kJ/mol
Kinetic Energy: 3620.3955078125 kJ/mol
Temperature: 306.42751154870894 K
Total Energy: -12187.996959788274 kJ/mol
------------------------------------------------------------
Step: 9050 / 10000 Time: 18.1 ps
Potential Energy -15863.94611124463 kJ/mol
Kinetic Energy: 3660.688720703125 kJ/mol
Temperature: 309.8378983232293 K
Total Energy: -12203.257390541505 kJ/mol
------------------------------------------------------------
Step: 9100 / 10000 Time: 18.2 ps
Potential Energy -15808.437625837993 kJ/mol
Kinetic Energy: 3575.87548828125 kJ/mol
Temperature: 302.65937108736375 K
Total Energy: -12232.562137556743 kJ/mol
------------------------------------------------------------
Step: 9150 / 10000 Time: 18.3 ps
Potential Energy -15874.946909619044 kJ/mol
Kinetic Energy: 3616.061279296875 kJ/mol
Temperature: 306.06066575640244 K
Total Energy: -12258.88563032217 kJ/mol
------------------------------------------------------------
Step: 9200 / 10000 Time: 18.4 ps
Potential Energy -15831.473052916597 kJ/mol
Kinetic Energy: 3722.62548828125 kJ/mol
Temperature: 315.08017904128354 K
Total Energy: -12108.847564635347 kJ/mol
------------------------------------------------------------
Step: 9250 / 10000 Time: 18.5 ps
Potential Energy -16007.393322435688 kJ/mol
Kinetic Energy: 3856.83447265625 kJ/mol
Temperature: 326.43952500797855 K
Total Energy: -12150.558849779438 kJ/mol
------------------------------------------------------------
Step: 9300 / 10000 Time: 18.6 ps
Potential Energy -15992.163736180883 kJ/mol
Kinetic Energy: 3676.6572265625 kJ/mol
Temperature: 311.1894604669454 K
Total Energy: -12315.506509618383 kJ/mol
------------------------------------------------------------
Step: 9350 / 10000 Time: 18.7 ps
Potential Energy -15789.817021002542 kJ/mol
Kinetic Energy: 3537.72314453125 kJ/mol
Temperature: 299.43018584231646 K
Total Energy: -12252.093876471292 kJ/mol
------------------------------------------------------------
Step: 9400 / 10000 Time: 18.8 ps
Potential Energy -15871.212102060686 kJ/mol
Kinetic Energy: 3582.02783203125 kJ/mol
Temperature: 303.18010076494636 K
Total Energy: -12289.184270029436 kJ/mol
------------------------------------------------------------
Step: 9450 / 10000 Time: 18.9 ps
Potential Energy -15794.094367710422 kJ/mol
Kinetic Energy: 3550.223876953125 kJ/mol
Temperature: 300.4882382899856 K
Total Energy: -12243.870490757297 kJ/mol
------------------------------------------------------------
Step: 9500 / 10000 Time: 19.0 ps
Potential Energy -15951.274566491615 kJ/mol
Kinetic Energy: 3695.653076171875 kJ/mol
Temperature: 312.7972546742339 K
Total Energy: -12255.62149031974 kJ/mol
------------------------------------------------------------
Step: 9550 / 10000 Time: 19.1 ps
Potential Energy -15955.751673889827 kJ/mol
Kinetic Energy: 3644.536376953125 kJ/mol
Temperature: 308.470776280814 K
Total Energy: -12311.215296936702 kJ/mol
------------------------------------------------------------
Step: 9600 / 10000 Time: 19.2 ps
Potential Energy -15854.343014722239 kJ/mol
Kinetic Energy: 3487.18212890625 kJ/mol
Temperature: 295.1524328687275 K
Total Energy: -12367.160885815989 kJ/mol
------------------------------------------------------------
Step: 9650 / 10000 Time: 19.3 ps
Potential Energy -16096.841749755215 kJ/mol
Kinetic Energy: 3769.02490234375 kJ/mol
Temperature: 319.0073900208046 K
Total Energy: -12327.816847411465 kJ/mol
------------------------------------------------------------
Step: 9700 / 10000 Time: 19.4 ps
Potential Energy -15898.283829098116 kJ/mol
Kinetic Energy: 3545.315185546875 kJ/mol
Temperature: 300.0727703972286 K
Total Energy: -12352.968643551241 kJ/mol
------------------------------------------------------------
Step: 9750 / 10000 Time: 19.5 ps
Potential Energy -15878.243243315737 kJ/mol
Kinetic Energy: 3588.18115234375 kJ/mol
Temperature: 303.7009130980333 K
Total Energy: -12290.062090971987 kJ/mol
------------------------------------------------------------
Step: 9800 / 10000 Time: 19.6 ps
Potential Energy -15829.612921503853 kJ/mol
Kinetic Energy: 3463.14501953125 kJ/mol
Temperature: 293.11795028396267 K
Total Energy: -12366.467901972603 kJ/mol
------------------------------------------------------------
Step: 9850 / 10000 Time: 19.7 ps
Potential Energy -15859.8818749278 kJ/mol
Kinetic Energy: 3448.70947265625 kJ/mol
Temperature: 291.8961366182442 K
Total Energy: -12411.17240227155 kJ/mol
------------------------------------------------------------
Step: 9900 / 10000 Time: 19.8 ps
Potential Energy -16031.284985428225 kJ/mol
Kinetic Energy: 3554.112060546875 kJ/mol
Temperature: 300.8173311806674 K
Total Energy: -12477.17292488135 kJ/mol
------------------------------------------------------------
Step: 9950 / 10000 Time: 19.9 ps
Potential Energy -16135.870697823833 kJ/mol
Kinetic Energy: 3569.36328125 kJ/mol
Temperature: 302.1081828564177 K
Total Energy: -12566.507416573833 kJ/mol
------------------------------------------------------------
MD simulation completed!
Number of steps: 10000
Trajectory saved as ethanol_md.pdb
============================================================
Simulation Averages:
============================================================
Total Potential Energy: -16205.749852406758 ± 566.0868502962544 kJ/mol
Kinetic Energy: 3435.582100830078 ± 285.9529246785413 kJ/mol
Temperature: 290.78504588984504 ± 24.20283721494963 K
Total Energy: -12770.167751576684 ± 812.8207331804372 kJ/mol
============================================================
Elapsed time: 0 minutes, 1 seconds
Performance: 1155.23 ns/day
Trajectory saved as ethanol_md.pdb
Simulation state saved as output.xml
Last frame saved as last_frame.pdb
* Info * Simulation output saved as output
import py3Dmol as p3d
with open("../output_files/ethanol_md.pdb", "r") as f:
pdb_data = f.read()
view = p3d.view(width=600, height=450)
view.addModelsAsFrames(pdb_data, "pdb", {"keepH": True})
view.setStyle({"resn": "MOL"}, {"stick": {"radius": 0.20}, "sphere": {"scale": 0.40}})
view.setStyle({"resn": "S01"}, {"stick": {"radius": 0.05}})
view.animate({"loop": "forward", "reps": 0})
view.zoomTo()
view.show()Loading...
- de Gracia Trivino, J. A., Brumboiu, I. E., Carrasco-Busturia, D., Li, X., Li, C., Linares, M., Lindfeld, V., Rhee, Y. M., Rune, J., Van Hoorn, B., Norman, P., & Ahlquist, M. S. G. (2025). VeloxChem Quantum–Classical Interoperability for Modeling of Complex Molecular Systems. J. Phys. Chem. A, 129(32), 7575–7587. 10.1021/acs.jpca.5c03187