cp2k/benchmarks/QMMM_MQAE

QM/MM - MQAE

Description

This benchmark performs a short QM/MM MD simulation of 5 steps. The MQAE system is a solute-solvent system consisting of a N-(6-methoxyquinolyl) acetoethyl ester in solution. All 34 atoms of the ester are treated with QM whereas the remaining water atoms are treated with MM. The parameters for the organic molecule are created using the General Amber Force Field (GAFF) and the water molecules are modelled using the SPCE model. The BLYP functional as the XC functional are used and an energy cut-off of 400 Ry for the plane waves was found to be suitable. The QM/MM coupling is described with the Gaussian Expansion of the Electrostatic Potential (GEEP) method, and the bonds between theQM and MM atoms are treated using the Generalized Hybrid Orbital (GHO) method.

See also https://doi.org/10.1021/acs.jctc.9b00424.

Files description

MQAE.inp - CP2K input file.

MQAE.prmtop - Amber forcefield for MM atoms. The Amber14 forcefield and the SPCE water model are used.

MQAE.pdb - Atomic input coordinates.

Results

MD Energy file

#     Step Nr.          Time[fs]        Kin.[a.u.]          Temp[K]            Pot.[a.u.]        Cons Qty[a.u.]        UsedTime[s]
         0            0.000000        10.239105709       300.000000000      -191.999316391      -181.760210683         0.000000000
         1            1.000000         8.558243627       250.751692693      -189.793945191      -181.235701564        54.682023599
         2            2.000000         7.864790893       230.433920213      -189.199737393      -181.334946500         6.080494038
         3            3.000000         7.943162986       232.730178174      -189.464441104      -181.521278118         5.934209533
         4            4.000000         7.312439357       214.250332928      -188.490384990      -181.177945634         6.046523766
         5            5.000000         8.147939618       238.730017526      -189.781378934      -181.633439317         5.907074374

Best Configurations

The best configurations are shown below.

Machine Name	Architecture	Date	Commit No.	Fastest time (s)	Number of Cores	Number of Threads
ARCHER	Cray XC30	16/06/2020	6e0731f	72.439	384	6 OMP threads per MPI task