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Commit 06320f44 authored by Giovanni Bussi's avatar Giovanni Bussi
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Regtests for maxent

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include ../../scripts/test.make
TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 29.788 29.788 29.788 70.53 109.47 70.53 P 1 1
MODEL 1
ATOM 1 O5' A 1 29.350 26.420 9.100 1.00 0.00
ATOM 2 H5T A 1 29.230 27.270 8.660 1.00 0.00
ATOM 3 C5' A 1 30.060 26.570 10.350 1.00 0.00
ATOM 4 1H5' A 1 30.970 27.120 10.120 1.00 0.00
ATOM 5 2H5' A 1 30.390 25.620 10.780 1.00 0.00
ATOM 6 C4' A 1 29.220 27.360 11.340 1.00 0.00
ATOM 7 H4' A 1 29.860 27.720 12.140 1.00 0.00
ATOM 8 O4' A 1 28.780 28.590 10.690 1.00 0.00
ATOM 9 C1' A 1 27.340 28.670 10.650 1.00 0.00
ATOM 10 H1' A 1 26.950 29.160 11.540 1.00 0.00
ATOM 11 N9 A 1 26.790 29.220 9.370 1.00 0.00
ATOM 12 C8 A 1 25.550 29.810 9.110 1.00 0.00
ATOM 13 H8 A 1 24.830 29.860 9.920 1.00 0.00
ATOM 14 N7 A 1 25.230 30.180 7.890 1.00 0.00
ATOM 15 C5 A 1 26.420 29.860 7.250 1.00 0.00
ATOM 16 C6 A 1 26.900 30.020 5.950 1.00 0.00
ATOM 17 N6 A 1 26.180 30.390 4.930 1.00 0.00
ATOM 18 H61 A 1 25.230 30.680 5.070 1.00 0.00
ATOM 19 H62 A 1 16.590 2.340 3.980 1.00 0.00
ATOM 20 N1 A 1 28.070 29.570 5.520 1.00 0.00
ATOM 21 C2 A 1 28.870 29.070 6.460 1.00 0.00
ATOM 22 H2 A 1 29.840 28.770 6.120 1.00 0.00
ATOM 23 N3 A 1 28.620 28.890 7.780 1.00 0.00
ATOM 24 C4 A 1 27.350 29.300 8.090 1.00 0.00
ATOM 25 C3' A 1 28.010 26.690 11.870 1.00 0.00
ATOM 26 H3' A 1 28.030 25.610 11.800 1.00 0.00
ATOM 27 C2' A 1 26.990 27.200 10.850 1.00 0.00
ATOM 28 1H2' A 1 27.030 26.670 9.900 1.00 0.00
ATOM 29 O2' A 1 25.620 27.090 11.220 1.00 0.00
ATOM 30 2HO' A 1 25.520 26.140 11.090 1.00 0.00
ATOM 31 O3' A 1 27.570 27.090 13.220 1.00 0.00
ATOM 32 H3T A 1 26.670 26.760 13.330 1.00 0.00
TER
ENDMDL
#! FIELDS time j1 j2 j3 j4 j5 j6 j7
0.000000 10.593483 3.991452 1.118545 4.535487 0.475877 3.268256 2.494038
10.000000 0.434136 5.242676 8.251033 2.614029 2.163582 1.404990 3.060875
20.000000 8.773931 5.879753 0.553086 2.525985 0.801487 5.792088 3.228069
30.000000 11.029838 4.528773 0.806521 1.946002 2.278457 5.655640 3.855359
40.000000 11.409602 5.596347 1.285364 6.497764 0.862320 5.707814 3.940420
50.000000 10.884786 7.565206 7.428449 1.896450 2.445897 0.199139 0.485447
60.000000 9.955792 6.507668 3.312648 2.071214 1.027960 5.799985 3.992038
70.000000 10.813602 6.746135 1.546803 2.864772 0.867356 5.453021 3.726299
80.000000 9.101818 4.966712 2.885810 1.886507 1.283637 5.363055 3.999512
90.000000 3.487607 7.466811 8.803344 2.460335 1.176599 5.220447 3.965647
100.000000 3.532403 4.893175 11.478312 2.051419 2.229474 5.371195 3.878713
type=driver
plumed_needs="matheval"
arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.4f"
This diff is collapsed.
MOLINFO STRUCTURE=ref.pdb MOLTYPE=rna
g1: TORSION ATOMS=@gamma-1
c1: TORSION ATOMS=@chi-1
puck1: PUCKERING ATOMS=@sugar-1
#J coupling
n1: TORSION ATOMS=10,9,27,28
n2: TORSION ATOMS=28,27,25,26
n3: TORSION ATOMS=26,25,6,7
x: TORSION ATOMS=29,25,9,28
#h4'-h5'
n4: TORSION ATOMS=7,6,3,4
#h4'-h5''
n5: TORSION ATOMS=7,6,3,5
chi: TORSION ATOMS=8,9,11,24
chi1: TORSION ATOMS=10,9,11,12
j1: MATHEVAL ARG=n1 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j2: MATHEVAL ARG=n2 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j3: MATHEVAL ARG=n3 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
#jh4'-h5'
j4: MATHEVAL ARG=n4 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)+1.373+0.27*cos(x)*sin(x) PERIODIC=NO
#jh4'-h5''
j5: MATHEVAL ARG=n5 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)+1.373-4.752*cos(x)*sin(x) PERIODIC=NO
#jc4-jh'
j6: MATHEVAL ARG=c1 FUNC=3.6*cos(x-(pi/180.0)*68.6)*cos(x-(pi/180.0)*68.6)+1.8*cos(x-(pi/180.0)*68.6)+0.4 PERIODIC=NO
#jc8-h1'
j7: MATHEVAL ARG=chi1 FUNC=4.2*cos(x+(pi/180.0)*(60.0-68.9))*cos(x+(pi/180.0)*(60.0-68.9))-0.5*cos(x+(pi/180.0)*(60.0-68.9))+0.3 PERIODIC=NO
MAXENT ...
LABEL=res
ARG=j1,j2,j3,j4,j5,j6,j7
KAPPA=0.001,0.001,0.001,0.001,0.001,0.001,0.001
TAU=3.0,3.0,3.0,3.0,3.0,3.0,3.0
ERROR_TYPE=LAPLACE
SIGMA=0.5
TSTART=50
TEND=100
TYPE=EQUAL AT=6.0,5.0,3.4,3.0,3.4,3.6,3.9
PACE=10
FMT=%f
TEMP=300
... MAXENT
PRINT ...
ARG=j1,j2,j3,j4,j5,j6,j7
STRIDE=10 FILE=colvar
... PRINT
TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 29.788 29.788 29.788 70.53 109.47 70.53 P 1 1
MODEL 1
ATOM 1 O5' A 1 29.350 26.420 9.100 1.00 0.00
ATOM 2 H5T A 1 29.230 27.270 8.660 1.00 0.00
ATOM 3 C5' A 1 30.060 26.570 10.350 1.00 0.00
ATOM 4 1H5' A 1 30.970 27.120 10.120 1.00 0.00
ATOM 5 2H5' A 1 30.390 25.620 10.780 1.00 0.00
ATOM 6 C4' A 1 29.220 27.360 11.340 1.00 0.00
ATOM 7 H4' A 1 29.860 27.720 12.140 1.00 0.00
ATOM 8 O4' A 1 28.780 28.590 10.690 1.00 0.00
ATOM 9 C1' A 1 27.340 28.670 10.650 1.00 0.00
ATOM 10 H1' A 1 26.950 29.160 11.540 1.00 0.00
ATOM 11 N9 A 1 26.790 29.220 9.370 1.00 0.00
ATOM 12 C8 A 1 25.550 29.810 9.110 1.00 0.00
ATOM 13 H8 A 1 24.830 29.860 9.920 1.00 0.00
ATOM 14 N7 A 1 25.230 30.180 7.890 1.00 0.00
ATOM 15 C5 A 1 26.420 29.860 7.250 1.00 0.00
ATOM 16 C6 A 1 26.900 30.020 5.950 1.00 0.00
ATOM 17 N6 A 1 26.180 30.390 4.930 1.00 0.00
ATOM 18 H61 A 1 25.230 30.680 5.070 1.00 0.00
ATOM 19 H62 A 1 16.590 2.340 3.980 1.00 0.00
ATOM 20 N1 A 1 28.070 29.570 5.520 1.00 0.00
ATOM 21 C2 A 1 28.870 29.070 6.460 1.00 0.00
ATOM 22 H2 A 1 29.840 28.770 6.120 1.00 0.00
ATOM 23 N3 A 1 28.620 28.890 7.780 1.00 0.00
ATOM 24 C4 A 1 27.350 29.300 8.090 1.00 0.00
ATOM 25 C3' A 1 28.010 26.690 11.870 1.00 0.00
ATOM 26 H3' A 1 28.030 25.610 11.800 1.00 0.00
ATOM 27 C2' A 1 26.990 27.200 10.850 1.00 0.00
ATOM 28 1H2' A 1 27.030 26.670 9.900 1.00 0.00
ATOM 29 O2' A 1 25.620 27.090 11.220 1.00 0.00
ATOM 30 2HO' A 1 25.520 26.140 11.090 1.00 0.00
ATOM 31 O3' A 1 27.570 27.090 13.220 1.00 0.00
ATOM 32 H3T A 1 26.670 26.760 13.330 1.00 0.00
TER
ENDMDL
#! FIELDS time j1_coupling j2_coupling j3_coupling j4_coupling j5_coupling j6_coupling j7_coupling
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
10.000000 0.004593 -0.001009 -0.002281 0.001535 -0.002924 -0.000332 -0.001406
20.000000 0.003309 -0.000952 -0.001162 0.001446 -0.003209 -0.000838 -0.001600
30.000000 0.003670 -0.000838 -0.001533 0.001384 -0.003548 -0.000552 -0.001687
40.000000 0.004128 -0.000881 -0.001769 0.001289 -0.003650 -0.000365 -0.001691
50.000000 0.004505 -0.000839 -0.001916 0.001533 -0.003827 -0.000218 -0.001688
60.000000 0.004781 -0.000694 -0.001688 0.001470 -0.003881 -0.000411 -0.001882
70.000000 0.004970 -0.000622 -0.001692 0.001426 -0.003994 -0.000306 -0.001877
80.000000 0.005168 -0.000550 -0.001769 0.001420 -0.004098 -0.000230 -0.001884
90.000000 0.005280 -0.000551 -0.001787 0.001380 -0.004174 -0.000166 -0.001881
100.000000 0.005199 -0.000472 -0.001613 0.001363 -0.004246 -0.000114 -0.001879
File added
include ../../scripts/test.make
#! FIELDS time j1 j2 j3 j4 j5 j6 j7
0.000000 10.593483 3.991452 1.118545 4.535487 0.475877 3.268256 2.494038
10.000000 0.434136 5.242676 8.251033 2.614029 2.163582 1.404990 3.060875
20.000000 8.773931 5.879753 0.553086 2.525985 0.801487 5.792088 3.228069
30.000000 11.029838 4.528773 0.806521 1.946002 2.278457 5.655640 3.855359
40.000000 11.409602 5.596347 1.285364 6.497764 0.862320 5.707814 3.940420
50.000000 10.884786 7.565206 7.428449 1.896450 2.445897 0.199139 0.485447
60.000000 9.955792 6.507668 3.312648 2.071214 1.027960 5.799985 3.992038
70.000000 10.813602 6.746135 1.546803 2.864772 0.867356 5.453021 3.726299
80.000000 9.101818 4.966712 2.885810 1.886507 1.283637 5.363055 3.999512
90.000000 3.487607 7.466811 8.803344 2.460335 1.176599 5.220447 3.965647
100.000000 3.532403 4.893175 11.478312 2.051419 2.229474 5.371195 3.878713
#! FIELDS time j1 j2 j3 j4 j5 j6 j7
0.000000 10.593483 3.991452 1.118545 4.535487 0.475877 3.268256 2.494038
10.000000 0.434136 5.242676 8.251033 2.614029 2.163582 1.404990 3.060875
20.000000 8.773931 5.879753 0.553086 2.525985 0.801487 5.792088 3.228069
30.000000 11.029838 4.528773 0.806521 1.946002 2.278457 5.655640 3.855359
40.000000 11.409602 5.596347 1.285364 6.497764 0.862320 5.707814 3.940420
50.000000 10.884786 7.565206 7.428449 1.896450 2.445897 0.199139 0.485447
60.000000 9.955792 6.507668 3.312648 2.071214 1.027960 5.799985 3.992038
70.000000 10.813602 6.746135 1.546803 2.864772 0.867356 5.453021 3.726299
80.000000 9.101818 4.966712 2.885810 1.886507 1.283637 5.363055 3.999512
90.000000 3.487607 7.466811 8.803344 2.460335 1.176599 5.220447 3.965647
100.000000 3.532403 4.893175 11.478312 2.051419 2.229474 5.371195 3.878713
#! FIELDS time j1 j2 j3 j4 j5 j6 j7
0.000000 10.593483 3.991452 1.118545 4.535487 0.475877 3.268256 2.494038
10.000000 0.434136 5.242676 8.251033 2.614029 2.163582 1.404990 3.060875
20.000000 8.773931 5.879753 0.553086 2.525985 0.801487 5.792088 3.228069
30.000000 11.029838 4.528773 0.806521 1.946002 2.278457 5.655640 3.855359
40.000000 11.409602 5.596347 1.285364 6.497764 0.862320 5.707814 3.940420
50.000000 10.884786 7.565206 7.428449 1.896450 2.445897 0.199139 0.485447
60.000000 9.955792 6.507668 3.312648 2.071214 1.027960 5.799985 3.992038
70.000000 10.813602 6.746135 1.546803 2.864772 0.867356 5.453021 3.726299
80.000000 9.101818 4.966712 2.885810 1.886507 1.283637 5.363055 3.999512
90.000000 3.487607 7.466811 8.803344 2.460335 1.176599 5.220447 3.965647
100.000000 3.532403 4.893175 11.478312 2.051419 2.229474 5.371195 3.878713
type=driver
plumed_needs="matheval"
arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.4f"
This diff is collapsed.
RESTART
MOLINFO STRUCTURE=ref.pdb MOLTYPE=rna
g1: TORSION ATOMS=@gamma-1
c1: TORSION ATOMS=@chi-1
puck1: PUCKERING ATOMS=@sugar-1
#J coupling
n1: TORSION ATOMS=10,9,27,28
n2: TORSION ATOMS=28,27,25,26
n3: TORSION ATOMS=26,25,6,7
x: TORSION ATOMS=29,25,9,28
#h4'-h5'
n4: TORSION ATOMS=7,6,3,4
#h4'-h5''
n5: TORSION ATOMS=7,6,3,5
chi: TORSION ATOMS=8,9,11,24
chi1: TORSION ATOMS=10,9,11,12
j1: MATHEVAL ARG=n1 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j2: MATHEVAL ARG=n2 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
j3: MATHEVAL ARG=n3 FUNC=9.67*cos(x)*cos(x)-2.03*cos(x) PERIODIC=NO
#jh4'-h5'
j4: MATHEVAL ARG=n4 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)+1.373+0.27*cos(x)*sin(x) PERIODIC=NO
#jh4'-h5''
j5: MATHEVAL ARG=n5 FUNC=8.313*cos(x)*cos(x)-0.99*cos(x)+1.373-4.752*cos(x)*sin(x) PERIODIC=NO
#jc4-jh'
j6: MATHEVAL ARG=c1 FUNC=3.6*cos(x-(pi/180.0)*68.6)*cos(x-(pi/180.0)*68.6)+1.8*cos(x-(pi/180.0)*68.6)+0.4 PERIODIC=NO
#jc8-h1'
j7: MATHEVAL ARG=chi1 FUNC=4.2*cos(x+(pi/180.0)*(60.0-68.9))*cos(x+(pi/180.0)*(60.0-68.9))-0.5*cos(x+(pi/180.0)*(60.0-68.9))+0.3 PERIODIC=NO
MAXENT ...
LABEL=res
ARG=j1,j2,j3,j4,j5,j6,j7
KAPPA=0.001,0.001,0.001,0.001,0.001,0.001,0.001
TAU=3.0,3.0,3.0,3.0,3.0,3.0,3.0
ERROR_TYPE=LAPLACE
SIGMA=0.5
TSTART=50
TEND=100
TYPE=EQUAL AT=6.0,5.0,3.4,3.0,3.4,3.6,3.9
PACE=10
FMT=%f
TEMP=300
... MAXENT
PRINT ...
ARG=j1,j2,j3,j4,j5,j6,j7
STRIDE=10 FILE=colvar
... PRINT
TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 29.788 29.788 29.788 70.53 109.47 70.53 P 1 1
MODEL 1
ATOM 1 O5' A 1 29.350 26.420 9.100 1.00 0.00
ATOM 2 H5T A 1 29.230 27.270 8.660 1.00 0.00
ATOM 3 C5' A 1 30.060 26.570 10.350 1.00 0.00
ATOM 4 1H5' A 1 30.970 27.120 10.120 1.00 0.00
ATOM 5 2H5' A 1 30.390 25.620 10.780 1.00 0.00
ATOM 6 C4' A 1 29.220 27.360 11.340 1.00 0.00
ATOM 7 H4' A 1 29.860 27.720 12.140 1.00 0.00
ATOM 8 O4' A 1 28.780 28.590 10.690 1.00 0.00
ATOM 9 C1' A 1 27.340 28.670 10.650 1.00 0.00
ATOM 10 H1' A 1 26.950 29.160 11.540 1.00 0.00
ATOM 11 N9 A 1 26.790 29.220 9.370 1.00 0.00
ATOM 12 C8 A 1 25.550 29.810 9.110 1.00 0.00
ATOM 13 H8 A 1 24.830 29.860 9.920 1.00 0.00
ATOM 14 N7 A 1 25.230 30.180 7.890 1.00 0.00
ATOM 15 C5 A 1 26.420 29.860 7.250 1.00 0.00
ATOM 16 C6 A 1 26.900 30.020 5.950 1.00 0.00
ATOM 17 N6 A 1 26.180 30.390 4.930 1.00 0.00
ATOM 18 H61 A 1 25.230 30.680 5.070 1.00 0.00
ATOM 19 H62 A 1 16.590 2.340 3.980 1.00 0.00
ATOM 20 N1 A 1 28.070 29.570 5.520 1.00 0.00
ATOM 21 C2 A 1 28.870 29.070 6.460 1.00 0.00
ATOM 22 H2 A 1 29.840 28.770 6.120 1.00 0.00
ATOM 23 N3 A 1 28.620 28.890 7.780 1.00 0.00
ATOM 24 C4 A 1 27.350 29.300 8.090 1.00 0.00
ATOM 25 C3' A 1 28.010 26.690 11.870 1.00 0.00
ATOM 26 H3' A 1 28.030 25.610 11.800 1.00 0.00
ATOM 27 C2' A 1 26.990 27.200 10.850 1.00 0.00
ATOM 28 1H2' A 1 27.030 26.670 9.900 1.00 0.00
ATOM 29 O2' A 1 25.620 27.090 11.220 1.00 0.00
ATOM 30 2HO' A 1 25.520 26.140 11.090 1.00 0.00
ATOM 31 O3' A 1 27.570 27.090 13.220 1.00 0.00
ATOM 32 H3T A 1 26.670 26.760 13.330 1.00 0.00
TER
ENDMDL
#! FIELDS time j1_coupling j2_coupling j3_coupling j4_coupling j5_coupling j6_coupling j7_coupling
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
10.000000 0.004593 -0.001009 -0.002281 0.001535 -0.002924 -0.000332 -0.001406
20.000000 0.003309 -0.000952 -0.001162 0.001446 -0.003209 -0.000838 -0.001600
30.000000 0.003670 -0.000838 -0.001533 0.001384 -0.003548 -0.000552 -0.001687
40.000000 0.004128 -0.000881 -0.001769 0.001289 -0.003650 -0.000365 -0.001691
50.000000 0.004505 -0.000839 -0.001916 0.001533 -0.003827 -0.000218 -0.001688
60.000000 0.004781 -0.000694 -0.001688 0.001470 -0.003881 -0.000411 -0.001882
70.000000 0.004970 -0.000622 -0.001692 0.001426 -0.003994 -0.000306 -0.001877
80.000000 0.005168 -0.000550 -0.001769 0.001420 -0.004098 -0.000230 -0.001884
90.000000 0.005280 -0.000551 -0.001787 0.001380 -0.004174 -0.000166 -0.001881
100.000000 0.005199 -0.000472 -0.001613 0.001363 -0.004246 -0.000114 -0.001879
#! FIELDS time j1_coupling j2_coupling j3_coupling j4_coupling j5_coupling j6_coupling j7_coupling
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
10.000000 0.004593 -0.001009 -0.002281 0.001535 -0.002924 -0.000332 -0.001406
20.000000 0.003309 -0.000952 -0.001162 0.001446 -0.003209 -0.000838 -0.001600
30.000000 0.003670 -0.000838 -0.001533 0.001384 -0.003548 -0.000552 -0.001687
40.000000 0.004128 -0.000881 -0.001769 0.001289 -0.003650 -0.000365 -0.001691
50.000000 0.004505 -0.000839 -0.001916 0.001533 -0.003827 -0.000218 -0.001688
60.000000 0.004781 -0.000694 -0.001688 0.001470 -0.003881 -0.000411 -0.001882
70.000000 0.004970 -0.000622 -0.001692 0.001426 -0.003994 -0.000306 -0.001877
80.000000 0.005168 -0.000550 -0.001769 0.001420 -0.004098 -0.000230 -0.001884
90.000000 0.005280 -0.000551 -0.001787 0.001380 -0.004174 -0.000166 -0.001881
100.000000 0.005199 -0.000472 -0.001613 0.001363 -0.004246 -0.000114 -0.001879
#! FIELDS time j1_coupling j2_coupling j3_coupling j4_coupling j5_coupling j6_coupling j7_coupling
10.000000 0.009791 -0.001480 -0.003894 0.002898 -0.007169 -0.000446 -0.003284
20.000000 0.008506 -0.001424 -0.002774 0.002809 -0.007454 -0.000952 -0.003478
30.000000 0.008868 -0.001310 -0.003146 0.002747 -0.007793 -0.000666 -0.003565
40.000000 0.009325 -0.001352 -0.003381 0.002651 -0.007894 -0.000479 -0.003569
50.000000 0.009702 -0.001311 -0.003529 0.002895 -0.008071 -0.000332 -0.003567
60.000000 0.009978 -0.001166 -0.003301 0.002833 -0.008125 -0.000525 -0.003760
70.000000 0.010167 -0.001094 -0.003305 0.002788 -0.008238 -0.000420 -0.003755
80.000000 0.010364 -0.001022 -0.003381 0.002783 -0.008342 -0.000344 -0.003762
90.000000 0.010476 -0.001023 -0.003400 0.002742 -0.008419 -0.000280 -0.003759
100.000000 0.010395 -0.000944 -0.003225 0.002725 -0.008490 -0.000228 -0.003757
File added
include ../../scripts/test.make
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