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benchmarks: add QMMM benchmarks

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QMMM_ClC
QMMM_MQAE
QMMM_CBD_PHY
This commit is contained in:
holly-t 2020-06-16 16:38:40 +01:00 • committed by Ole Schütt
parent 574527f47f
commit a4ee7f8f37
13 changed files with 1243605 additions and 19 deletions
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21
benchmarks/QMMM_CBD_PHY/README.md
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@ -22,10 +22,23 @@ the TIP3P water model are used.
## 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 239.300084734 300.000000000 -1095.757596412 -856.457511678 0.000000000
1 1.000000 218.500201290 273.924100193 -1067.608771800 -849.108570511 182.675886658
2 2.000000 218.405643404 273.805557127 -1068.870854087 -850.465210683 23.324723621
3 3.000000 235.615216194 295.380442246 -1089.654654224 -854.039438030 24.849245982
4 4.000000 237.524625019 297.774184180 -1087.284636223 -849.760011204 26.518459213
5 5.000000 245.799648725 308.148217747 -1101.835669561 -856.036020836 27.761591604
``
### Best Configurations
The best configurations are shown below.
| Machine Name | Architecture | Date | Fastest time (s) | Number of Cores | Number of Threads |
| ------------ | ------------ | ---------- | ---------------- | --------------- | --------------------------------- |
| ARCHER | Cray XC30 | | | | 1 OMP thread per MPI task |
| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
| ARCHER | Cray XC30 | 07/06/2020 | 6e0731f | 358.478 | 576 | 6 OMP threads per MPI task |

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benchmarks/QMMM_CBD_PHY/CBD_PHY-cp2k.inp → benchmarks/QMMM_CBD_PHY/cbd_phy.inp
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@ -88,7 +88,7 @@
&FORCEFIELD
PARMTYPE AMBER
DO_NONBONDED .TRUE.
PARM_FILE_NAME CBD_PHY.prmtop
PARM_FILE_NAME cbd_phy.prmtop
EI_SCALE14 1.0
VDW_SCALE14 1.0
&SPLINE
@ -118,9 +118,9 @@
&END CELL
&TOPOLOGY ! Section used to center the atomic coordinates in the given box. Useful for big molecules
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME CBD_PHY.prmtop
CONN_FILE_NAME cbd_phy.prmtop
COORD_FILE_FORMAT PDB
COORD_FILE_NAME CBD_PHY.pdb
COORD_FILE_NAME cbd_phy.pdb
&CENTER_COORDINATES
CENTER_POINT 9.5 11.7 15.3
&END CENTER_COORDINATES
@ -149,18 +149,6 @@
&END FORCE_EVAL
#&MOTION
# &GEO_OPT
# OPTIMIZER LBFGS
# &END
# &CONSTRAINT
# &FIXED_ATOMS
# LIST 1..167923
# EXCLUDE_MM .FALSE.
# EXCLUDE_QM .TRUE.
# &END FIXED_ATOMS
# &END CONSTRAINT
#&END MOTION
&MOTION
&MD
ENSEMBLE NVE

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&GLOBAL
PROJECT CIC
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
&DFT
CHARGE 1
MULTIPLICITY 1
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 400
COMMENSURATE
&END MGRID
&SCF ! Parameters controlling the convergence of the scf. This section should not be changed.
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 300
&OT T
MINIMIZER DIIS
STEPSIZE 1.4999999999999999E-01
PRECONDITIONER FULL_ALL
&END OT
&END SCF
&XC ! Parameters needed to compute the electronic exchange potential
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&QS
METHOD GPW
EPS_DEFAULT 1.0E-12
&END QS
&END DFT
&QMMM ! This defines the QS cell in the QMMM calc
&CELL
ABC 17.7 17.7 17.7
PERIODIC XYZ
&END CELL
CENTER EVERY_STEP
ECOUPL GAUSS
USE_GEEP_LIB 15
&PERIODIC # apply periodic potential
#turn on/off coupling/recoupling of the QM multipole
&MULTIPOLE ON
&END
&END PERIODIC
&QM_KIND O
MM_INDEX 2887 2888 2080 2079
&END QM_KIND
&QM_KIND C
MM_INDEX 2880 2883 2886 2072 2075 2078
&END QM_KIND
&QM_KIND H
MM_INDEX 2884 2885 2881 2882 2074 2073 2077 2076 2081
&END QM_KIND
&LINK
MM_INDEX 2878
QM_INDEX 2880
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2070
QM_INDEX 2072
LINK_TYPE IMOMM
&END LINK
&END QMMM
&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME ClC.prmtop
DO_NONBONDED .TRUE.
EI_SCALE14 1.0
VDW_SCALE14 1.0
&SPLINE
EMAX_SPLINE 1.0E14
RCUT_NB [angstrom] 12
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .40
GMAX 80
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 126.9338000 126.9338000 90.6262000
PERIODIC XYZ
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&TOPOLOGY ! Section used to center the atomic coordinates in the given box. Useful for big molecules
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME ClC.prmtop
COORD_FILE_FORMAT PDB
COORD_FILE_NAME ClC.pdb
&CENTER_COORDINATES
&END CENTER_COORDINATES
&END TOPOLOGY
&KIND H
ELEMENT H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND C
ELEMENT C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND O
ELEMENT O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND CL-
ELEMENT CL
&END KIND
&KIND NA+
ELEMENT NA
&END KIND
&KIND HX1
ELEMENT H
&END KIND
&KIND HX2
ELEMENT H
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 5
TEMPERATURE 300
TIMESTEP 1
&END MD
&END MOTION

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&GLOBAL
PROJECT CIC
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
&DFT
CHARGE 1
MULTIPLICITY 1
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 300
COMMENSURATE
&END MGRID
&SCF ! Parameters controlling the convergence of the scf. This section should not be changed.
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 300
&OT T
MINIMIZER DIIS
STEPSIZE 1.4999999999999999E-01
PRECONDITIONER FULL_ALL
&END OT
&END SCF
&XC ! Parameters needed to compute the electronic exchange potential
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&QS
METHOD GPW
EPS_DEFAULT 1.0E-12
&END QS
&END DFT
&QMMM ! This defines the QS cell in the QMMM calc
&CELL
ABC 27.517 25.316 25.316
PERIODIC XYZ
&END CELL
CENTER EVERY_STEP
ECOUPL GAUSS
USE_GEEP_LIB 15
&PERIODIC # apply periodic potential
#turn on/off coupling/recoupling of the QM multipole
&MULTIPOLE ON
&END
&END PERIODIC
PARALLEL_SCHEME GRID
&QM_KIND S
MM_INDEX 2901
&END QM_KIND
&QM_KIND H
MM_INDEX 1453 1455 1457 1459 1460 1461 1463 1464 1466 1467 1468 2069 2862
MM_INDEX 2071 2073 2074 2076 2077 2081 2085 2087 2088 2120 2122 2124 2126
MM_INDEX 2127 2128 2130 2131 2132 2623 2625 2627 2628 2630 2632 2633 2634
MM_INDEX 2636 2637 2638 2662 2664 2666 2667 2668 2672 2674 2676 2677 2680
MM_INDEX 2682 2684 2686 2688 2804 2806 2808 2809 2812 2814 2816 2818 2820
MM_INDEX 2866 2867 2869 2870 2877 2879 2881 2882 2884 2885 2892 2894 2896
MM_INDEX 2897 2899 2900 2903 2904 2905 5265 5266 5269 5271 5273 5275 5277
MM_INDEX 5904 5906 5907 5908 5910 5911 5913 5914 5915 5947 5948 5949 5986
MM_INDEX 5988 5990 5992 5993 5994 5996 6576 6578 6579 6582 6584 6587 6589
MM_INDEX 6591
&END QM_KIND
&QM_KIND N
MM_INDEX 1452 2068 2084 2119 2622 2661 2671 2803 2876 2891 5985 2861
&END QM_KIND
&QM_KIND O
MM_INDEX 1451 2067 2079 2080 2083 2670 2822 2872 2873 2875 2887 2888 2890
MM_INDEX 5995 6586
MM_INDEX 2118 2860 2802 5984 2621
&END QM_KIND
&QM_KIND C
MM_INDEX 1450 1454 1456 1458 1462 1465 2066 2070 2072 2075 2078 2082 2086
MM_INDEX 2121 2123 2125 2129 2624 2626 2629 2631 2635 2663 2665 2669 2673
MM_INDEX 2675 2678 2679 2681 2683 2685 2687 2805 2807 2810 2811 2813 2815
MM_INDEX 2817 2819 2863 2865 2868 2871 2874 2878 2880 2883 2886 2889 2893
MM_INDEX 2895 2898 2902 5264 5267 5268 5270 5272 5274 5276 5903 5905 5909
MM_INDEX 5912 5946 5987 5989 5991 6575 6577 6580 6581 6583 6585 6588 6590
MM_INDEX 2859 2801 5983 2620 2117
&END QM_KIND
&LINK
MM_INDEX 5968
QM_INDEX 5983
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2786
QM_INDEX 2801
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2844
QM_INDEX 2859
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2906
QM_INDEX 2893
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 5944
QM_INDEX 5946
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 6592
QM_INDEX 6575
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 1469
QM_INDEX 1454
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2617
QM_INDEX 2620
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 5901
QM_INDEX 5903
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 5262
QM_INDEX 5264
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2133
QM_INDEX 2121
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2107
QM_INDEX 2117
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2089
QM_INDEX 2086
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2046
QM_INDEX 2066
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2689
QM_INDEX 2673
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2639
QM_INDEX 2624
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 2821
QM_INDEX 2805
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 1447
QM_INDEX 1450
LINK_TYPE IMOMM
&END LINK
&LINK
MM_INDEX 5997
QM_INDEX 5987
LINK_TYPE IMOMM
&END LINK
&END QMMM
&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME ClC.prmtop
DO_NONBONDED .TRUE.
EI_SCALE14 1.0
VDW_SCALE14 1.0
&SPLINE
EMAX_SPLINE 1.0E14
RCUT_NB [angstrom] 12
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .40
GMAX 80
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 126.9338000 126.9338000 90.6262000
PERIODIC XYZ
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&TOPOLOGY ! Section used to center the atomic coordinates in the given box. Useful for big molecules
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME ClC.prmtop
COORD_FILE_FORMAT PDB
COORD_FILE_NAME ClC.pdb
&CENTER_COORDINATES
&END CENTER_COORDINATES
&END TOPOLOGY
&KIND H
ELEMENT H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND C
ELEMENT C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
ELEMENT N
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND O
ELEMENT O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND S
ELEMENT S
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND CL-
ELEMENT CL
&END KIND
&KIND NA+
ELEMENT NA
&END KIND
&KIND HX1
ELEMENT H
&END KIND
&KIND HX2
ELEMENT H
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 5
TEMPERATURE 300
TIMESTEP 1
&END MD
&END MOTION

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# QMMM_ClC
## Description
This benchmark performs of a short QM/MM MD simulation of 5 steps.
ClC consists of a (ClC-ec1) chloride ion channel embedded in a lipid bilayer (PDB-ID: 1KPK),
which is solvated in water. Two variants are included for this system - ClC-19 and ClC-253
which differ only in having respectively 19 and 253 atoms treated quantum mechanically,
representing a small and large QM subsystem within a large MM subsystem (150,925 atoms in total).
The QM regions are modelled using the GPW method with the DZVP-MOLOPT-GTH basis set and the BLYP
XC functional and the corresponding pseudopotentials. An energy cut-off for the plane waves of
300 Ry was found to be suitable. The Amber14 forcefield is used for the protein and
lipid14 forcefield is used for the lipid molecules, and water molecules are treated using the TIP3P model.
The QM/MM coupling is described with the Gaussian Expansion of the Electrostatic Potential (GEEP)
method, and the bonds between the QM and MM atoms are treated using the Generalized Hybrid Orbital (GHO) method.
## Files description
``ClC-19-cp2k.inp`` - ClC with 19 QM atoms.
``ClC-253-cp2k.inp`` - ClC with 253 QM atoms.
``ClC.prmtop`` - Amber forcefield for MM atoms. The Amber14 forcefield and
the TIP3P water model are used.
``ClC.pdb`` - Atomic input coordinates.
## Results
### MD Energy file
**ClC-19**
```
# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
0 0.000000 215.076797492 300.000000000 -596.086687006 -381.009889515 0.000000000
1 1.000000 198.652973057 277.091218635 -574.153507548 -375.500534491 70.967594760
2 2.000000 195.784312092 273.089865167 -572.000466754 -376.216154662 19.159191409
3 3.000000 207.799106381 289.848708188 -586.253625107 -378.454518727 14.798553064
4 4.000000 214.860114839 299.697760072 -590.496047349 -375.635932510 12.901749167
5 5.000000 229.995582697 320.809476493 -610.436739448 -380.441156751 15.286556874
```
**ClC-253**
```
# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
0 0.000000 215.076797492 300.000000000 -1491.612940400 -1276.536142909 0.000000000
1 1.000000 198.662217163 277.104112782 -1469.689644927 -1271.027427764 473.027817380
2 2.000000 195.807635290 273.122397543 -1467.549011288 -1271.741375998 105.500705595
3 3.000000 207.842602626 289.909378952 -1481.822393971 -1273.979791345 95.116800701
4 4.000000 214.921174580 299.782929288 -1486.080988136 -1271.159813556 86.241739729
5 5.000000 230.080097510 320.927362031 -1506.045017099 -1275.964919589 86.374744609
```
### Best Configurations
The best configurations are shown below.
**ClC-19**
| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 225.171 | 384 | 4 OMP threads per MPI task |
**ClC-253**
| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 937.151 | 576 | 6 OMP threads per MPI task |

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# QMMM_MQAE
## Description
This benchmark performs of 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.
## Files description
``mqae-cp2k.inp`` - The 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 |

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&GLOBAL
PROJECT MQAE
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
&DFT
CHARGE 1
MULTIPLICITY 1
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 400
COMMENSURATE
&END MGRID
&SCF ! Parameters controlling the convergence of the scf. This section should not be changed.
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 300
&OT T
MINIMIZER DIIS
STEPSIZE 1.4999999999999999E-01
PRECONDITIONER FULL_ALL
&END OT
&END SCF
&XC ! Parameters needed to compute the electronic exchange potential
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&QS
METHOD GPW
EPS_DEFAULT 1.0E-12
&END QS
&END DFT
&QMMM ! This defines the QS cell in the QMMM calc
&CELL
ABC 13.79565 17.3825 10.76061
PERIODIC XYZ
&END CELL
ECOUPL GAUSS
USE_GEEP_LIB 15
&PERIODIC # apply periodic potential
#turn on/off coupling/recoupling of the QM multipole
&MULTIPOLE ON
&END
&END PERIODIC
&QM_KIND O
MM_INDEX 1 3 28
&END QM_KIND
&QM_KIND N
MM_INDEX 14
&END QM_KIND
&QM_KIND C
MM_INDEX 2 4 7 11 15 17 19 21 22 23 25 27 29 33
&END QM_KIND
&QM_KIND H
MM_INDEX 5 6 8 9 10 12 13 16 18 20 24 26 30 31 32 34
&END QM_KIND
&END QMMM
&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME mqae.prmtop
EI_SCALE14 1.0
VDW_SCALE14 1.0
&SPLINE
EMAX_SPLINE 1.0E14
RCUT_NB [angstrom] 12
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .40
GMAX 80
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 41.751 41.751 41.751
PERIODIC XYZ
ALPHA_BETA_GAMMA 90 90 90
&END CELL
&TOPOLOGY ! Section used to center the atomic coordinates in the given box. Useful for big molecules
CONN_FILE_FORMAT AMBER
CONN_FILE_NAME mqae.prmtop
COORD_FILE_FORMAT PDB
COORD_FILE_NAME mqae.pdb
&END TOPOLOGY
&KIND H
ELEMENT H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND C
ELEMENT C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND O
ELEMENT O
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND N
ELEMENT N
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q5
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 5
TEMPERATURE 300
TIMESTEP 1
&END MD
&END MOTION

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