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add charmmfsw example for kokkos gpu testing

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alphataubio 2024-07-07 15:32:12 -04:00
parent 2cb3cb3323
commit 9c37e0f0df
3 changed files with 387 additions and 0 deletions
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340
examples/charmmfsw/charmmff.cmap Normal file
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#CMAP for C NH1 CT1 C NH1 CT1 C NH1; id=1
#phi = -180.000000
0.130000 0.770000 0.970000 1.250000 2.120000
2.720000 2.090000 1.790000 0.780000 -0.690000
1.000000 -2.200000 -4.830000 -4.820000 -4.910000
-3.590000 -2.770000 -2.780000 -2.450000 -2.350000
-2.340000 -1.520000 -0.950000 -0.040000
#phi = -165.000000
-0.130000 1.380000 1.580000 1.870000 2.400000
2.490000 2.440000 1.930000 1.090000 0.640000
0.260000 -2.800000 -4.010000 -4.140000 -3.420000
-2.600000 -2.300000 -1.500000 -1.100000 -0.860000
-0.640000 -0.210000 -1.080000 -1.120000
#phi = -150.000000
0.080000 1.420000 1.620000 2.050000 2.650000
2.720000 2.320000 1.990000 1.560000 2.460000
-0.230000 -1.820000 -2.580000 -3.010000 -2.550000
-1.890000 -1.350000 -0.730000 0.070000 -0.230000
-0.770000 -1.280000 -1.290000 -0.820000
#phi = -135.000000
0.930000 1.520000 2.240000 2.550000 3.110000
2.920000 2.460000 2.190000 2.060000 1.850000
0.120000 -1.180000 -2.000000 -2.280000 -1.960000
-1.340000 -0.930000 0.020000 0.310000 -0.520000
-1.150000 -0.980000 -0.570000 -0.440000
#phi = -120.000000
1.360000 1.960000 2.700000 3.040000 3.700000
3.560000 2.640000 2.770000 2.720000 1.630000
0.710000 -0.790000 -2.120000 -2.630000 -1.800000
-0.430000 -0.060000 0.440000 0.910000 -0.550000
-0.970000 -0.860000 -0.250000 0.450000
#phi = -105.000000
2.050000 2.540000 2.820000 3.090000 3.370000
3.550000 3.070000 2.900000 2.960000 2.120000
0.910000 -0.820000 -2.090000 -2.240000 -1.460000
0.210000 0.080000 0.770000 1.040000 -0.120000
-0.320000 -0.160000 0.310000 0.730000
#phi = -90.000000
1.450000 2.750000 2.740000 3.160000 3.450000
3.340000 3.180000 3.900000 3.340000 2.440000
0.910000 -0.610000 -1.510000 -1.620000 -0.960000
-0.020000 0.420000 0.910000 0.460000 0.150000
-0.070000 0.020000 0.280000 0.750000
#phi = -75.000000
1.380000 3.350000 2.350000 3.060000 3.810000
3.700000 3.580000 4.210000 3.540000 1.690000
0.100000 -0.680000 -0.120000 -0.430000 -0.600000
0.230000 0.420000 0.300000 0.550000 0.190000
-0.250000 -0.190000 -0.250000 0.470000
#phi = -60.000000
0.240000 1.230000 1.720000 3.170000 4.210000
4.390000 4.280000 3.670000 2.270000 -0.480000
-0.410000 -0.040000 -0.360000 -0.820000 -0.170000
0.140000 0.270000 0.320000 0.310000 -0.670000
-0.950000 -1.530000 -1.480000 -0.200000
#phi = -45.000000
-1.180000 0.080000 2.350000 4.210000 5.380000
5.390000 4.380000 2.460000 1.120000 0.110000
0.010000 -0.150000 -0.800000 -0.580000 0.080000
0.270000 -0.050000 0.380000 0.250000 -0.890000
-1.580000 -1.950000 -1.980000 -2.000000
#phi = -30.000000
-1.170000 1.070000 4.180000 6.740000 6.070000
4.810000 2.780000 1.320000 0.770000 -0.010000
0.280000 -0.710000 1.310000 1.520000 1.920000
2.220000 0.190000 0.530000 0.330000 -1.600000
-2.850000 -3.550000 -3.280000 -2.660000
#phi = -15.000000
0.290000 5.590000 3.730000 3.220000 3.270000
2.520000 1.590000 1.380000 0.860000 0.660000
1.620000 0.850000 0.510000 0.740000 1.020000
1.620000 -0.340000 0.180000 -0.610000 -2.560000
-3.790000 -3.810000 -3.160000 -1.750000
#phi = 0.000000
2.830000 0.790000 0.320000 0.480000 0.630000
0.980000 1.240000 1.670000 1.650000 2.520000
1.610000 0.780000 0.120000 0.070000 0.120000
-1.570000 -1.210000 -1.930000 -2.600000 -3.790000
-3.930000 -3.620000 -2.680000 -0.920000
#phi = 15.000000
-0.780000 -1.910000 -2.050000 -1.850000 -1.050000
0.180000 1.680000 2.220000 1.360000 2.450000
1.440000 0.680000 -0.240000 -0.540000 -0.790000
-2.180000 -3.210000 -4.350000 -3.940000 -3.910000
-3.460000 -2.770000 1.760000 0.310000
#phi = 30.000000
-2.960000 -3.480000 -3.440000 -2.400000 -1.130000
0.340000 1.430000 1.390000 0.970000 2.460000
1.520000 0.550000 -0.410000 -1.480000 -3.580000
-4.130000 -4.560000 -4.440000 -3.580000 -2.960000
-1.960000 -1.070000 -1.600000 -2.450000
#phi = 45.000000
-4.020000 -3.840000 -3.370000 -2.330000 -0.980000
0.360000 0.810000 0.750000 0.500000 1.900000
0.770000 -0.420000 -3.290000 -3.910000 -4.520000
-4.890000 -3.850000 -4.150000 -2.670000 -2.370000
-2.860000 -3.420000 -3.670000 -3.600000
#phi = 60.000000
-3.350000 -2.980000 -2.320000 -1.240000 -0.260000
0.720000 0.670000 0.440000 2.400000 1.630000
-2.010000 -3.310000 -3.990000 -4.530000 -4.850000
-3.770000 -3.940000 -3.890000 -2.610000 -3.510000
-3.760000 -3.640000 -3.450000 -3.340000
#phi = 75.000000
-2.250000 -1.640000 -1.010000 0.040000 0.640000
0.820000 0.520000 -0.010000 -0.370000 -1.190000
-2.390000 -3.380000 -4.500000 -5.590000 -5.510000
-4.940000 -3.830000 -3.840000 -3.700000 -4.150000
-4.170000 -3.730000 -3.740000 -2.620000
#phi = 90.000000
-1.720000 -1.180000 -0.430000 0.280000 0.810000
0.800000 0.480000 -0.340000 -0.790000 -1.770000
-2.810000 -3.800000 -5.220000 -6.280000 -6.580000
-5.640000 -5.060000 -4.020000 -4.150000 -4.470000
-4.100000 -3.770000 -3.160000 -2.650000
#phi = 105.000000
-1.850000 -1.090000 -0.450000 0.130000 1.010000
0.880000 0.490000 -0.220000 -0.860000 -1.680000
-3.010000 -4.130000 -5.990000 -6.860000 -6.830000
-5.850000 -3.860000 -4.860000 -4.910000 -4.720000
-4.600000 -4.090000 -3.270000 -2.410000
#phi = 120.000000
-1.970000 -1.120000 -0.540000 -0.150000 0.760000
1.040000 0.760000 0.310000 -0.330000 -1.870000
-3.370000 -5.010000 -6.120000 -7.050000 -6.980000
-3.700000 -4.510000 -5.090000 -5.420000 -4.850000
-4.440000 -4.000000 -3.420000 -2.750000
#phi = 135.000000
-2.110000 -1.170000 -0.320000 -0.010000 0.320000
1.090000 0.940000 0.630000 -0.170000 -1.830000
-3.470000 -4.950000 -6.110000 -1.920000 -4.050000
-5.000000 -5.000000 -4.840000 -4.890000 -4.300000
-4.490000 -4.440000 -4.160000 -3.180000
#phi = 150.000000
-1.760000 -0.400000 0.020000 0.360000 0.630000
1.260000 1.360000 0.950000 -0.070000 -1.480000
-3.150000 1.840000 -1.760000 -5.090000 -5.740000
-5.390000 -4.780000 -4.190000 -4.120000 -4.040000
-4.130000 -4.030000 -4.030000 -2.940000
#phi = 165.000000
-0.810000 -0.070000 0.380000 0.540000 1.280000
1.640000 1.700000 1.520000 0.630000 -1.090000
-2.740000 -0.740000 -4.560000 -6.410000 -5.890000
-5.140000 -4.190000 -3.670000 -3.840000 -3.560000
-3.550000 -3.250000 -2.750000 -1.810000
#CMAP for C NH1 CT2 C NH1 CT2 C NH1; id=2
#phi = -180.000000
0.235350 0.182300 0.177200 0.396800 0.859400
1.489700 2.092500 2.297700 1.808600 0.696200
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
0.696200 1.808200 2.301700 2.092600 1.489100
0.859500 0.396900 0.176900 0.182400
#phi = -165.000000
0.020100 -0.203800 -0.269700 0.014200 0.620800
1.392400 2.046200 2.188200 1.683900 0.688500
-0.373700 -0.703500 0.837800 3.704000 -0.730100
0.594100 1.713100 2.205800 2.026400 1.529800
1.027400 0.623800 0.348400 0.182800
#phi = -150.000000
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
1.168000 1.641000 1.618100 1.302200 0.615100
0.065700 0.738500 2.959500 -2.036600 -0.934600
0.407900 1.517000 1.984800 1.833100 1.435200
0.995600 0.562200 0.150600 -0.209000
#phi = -135.000000
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
0.454400 0.737600 0.879300 0.850100 0.670300
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
0.279600 1.322000 1.668300 1.521300 1.193900
0.765300 0.246000 -0.315500 -0.823200
#phi = -120.000000
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
-0.401000 -0.015100 0.321300 0.634600 0.976300
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
0.308700 1.098100 1.245300 1.133600 0.881800
0.448200 -0.153900 -0.823700 -1.404300
#phi = -105.000000
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
-0.980600 -0.429100 0.144700 0.734000 -0.918300
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
0.107000 0.496000 0.553500 0.584300 0.494000
0.098300 -0.529800 -1.237900 -1.840100
#phi = -90.000000
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
-0.439600 -1.038600 -1.741000 -2.373200
#phi = -75.000000
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
-1.360700 -2.009200 -2.745700 -3.424900
#phi = -60.000000
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
-0.174700 0.262600 0.039200 -0.663000 -1.530700
-2.478200 -3.465600 -4.334200 -5.011200
#phi = -45.000000
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
0.768200 0.568500 -0.831300 -2.343900 -3.037100
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
0.077000 0.441500 0.257500 -0.491100 -1.820600
-3.473100 -4.895200 -5.790700 -6.205900
#phi = -30.000000
-5.258225 -3.675795 -1.631110 0.430085 1.496470
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
0.054300 0.497200 0.599600 -0.171000 -2.137600
-4.237000 -5.584100 -6.135100 -6.067000
#phi = -15.000000
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
-0.197100 0.549500 0.850400 -0.689700 -2.819900
-4.393000 -5.111500 -5.205690 -4.654785
#phi = 0.000000
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
-3.450950 -3.620070 -3.412065 -2.349860
#phi = 15.000000
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
-2.819900 -0.689700 0.850400 0.549500 -0.197100
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
-1.560780 -1.452885 1.432450 -0.902080
#phi = 30.000000
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
-2.137600 -0.171000 0.599600 0.497200 0.054300
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
1.496470 0.430085 -1.631110 -3.675795
#phi = 45.000000
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
-1.820600 -0.491100 0.257500 0.441500 0.077000
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
-3.037100 -2.343900 -0.831300 0.568500 0.768200
-0.196160 -1.922530 -3.816620 -5.298400
#phi = 60.000000
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
-1.530700 -0.663000 0.039200 0.262600 -0.174700
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
-1.710200 -3.283200 -4.640100 -5.355100
#phi = 75.000000
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
-2.252200 -3.364700 -4.109000 -4.268200
#phi = 90.000000
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
-2.054300 -2.785300 -3.199500 -3.181100
#phi = 105.000000
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
0.494000 0.584300 0.553500 0.496000 0.107000
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
-0.918300 0.734000 0.144700 -0.429100 -0.980600
-1.577700 -2.135600 -2.473700 -2.487000
#phi = 120.000000
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
0.881800 1.133600 1.245300 1.098100 0.308700
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
0.976300 0.634600 0.321300 -0.015100 -0.401000
-0.896500 -1.447900 -1.860700 -1.965500
#phi = 135.000000
-1.208900 -0.823200 -0.315500 0.246000 0.765300
1.193900 1.521300 1.668300 1.322000 0.279600
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
0.670300 0.850100 0.879300 0.737600 0.454400
-0.112400 -0.817500 -1.319200 -1.429400
#phi = 150.000000
-0.533400 -0.209000 0.150600 0.562200 0.995600
1.435200 1.833100 1.984800 1.517000 0.407900
-0.934600 -2.036600 2.959500 0.738500 0.065700
0.615100 1.302200 1.618100 1.641000 1.168000
0.365300 -0.379800 -0.804600 -0.807400
#phi = 165.000000
0.019900 0.182800 0.348400 0.623800 1.027400
1.529800 2.026400 2.205800 1.713100 0.594100
-0.730100 3.704000 0.837800 -0.703500 -0.373700
0.688500 1.683900 2.188200 2.046200 1.392400
0.620800 0.014200 -0.269700 -0.203800

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#echo screen
#variable dcdfreq index 5000
#variable outputname index step5_production
#variable inputname index step4.1_equilibration
# charmmfsw example generated by https://charmm-gui.org/
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
#
# Dependencies: packages MOLECULE / KSPACE / RIGID
# To test with KOKKOS, use -sf kk
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
special_bonds charmm
improper_style harmonic
timestep 2
fix cmap all cmap charmmff.cmap
fix_modify cmap energy yes
read_data data.charmmfsw.gz fix cmap crossterm CMAP
#variable laststep file ${inputname}.dump
#next laststep
#read_dump ${inputname}.dump ${laststep} x y z vx vy vz ix iy iz box yes replace yes format native
neighbor 2 bin
neigh_modify delay 5 every 1
#include restraints/constraint_angletype
fix 1 all shake 1e-6 500 0 m 1.008 a 142
fix 2 all npt temp 303.15 303.15 100.0 iso 0.9869233 0.9869233 1000 couple xyz mtk no pchain 0
thermo 100
thermo_style custom step time spcpu cpuremain etotal pe ke temp press vol
run 1000