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Commit 1c7d139a authored by Carlo Camilloni's avatar Carlo Camilloni
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Merge branch 'master' into BayesBias

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regtest/secondarystructure/rt33-mpi/Makefile 0 → 100644
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include ../../scripts/test.make
regtest/secondarystructure/rt33-mpi/amyloid.pdb 0 → 100644
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regtest/secondarystructure/rt33-mpi/amyloid.xyz 0 → 100644
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regtest/secondarystructure/rt33-mpi/colvar.reference 0 → 100644
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#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum
0.000000 0.3042 0.1654 0.1654 0.2681 0.1425 0.1425 0.5722
0.050000 70.2841 42.5600 42.5600 14.6579 4.1424 4.1424 84.9420
0.100000 55.0842 34.0262 34.0262 13.0049 3.2851 3.2851 68.0891
0.150000 76.1957 47.7586 47.7586 16.2009 4.3921 4.3921 92.3966
0.200000 8.9531 2.2688 2.2688 57.6662 45.9216 45.9216 66.6193
0.250000 16.4632 4.8853 4.8853 100.7083 83.4592 83.4592 117.1715
regtest/secondarystructure/rt33-mpi/config 0 → 100644
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mpiprocs=2
type=driver
arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz amyloid.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
regtest/secondarystructure/rt33-mpi/forces.reference 0 → 100644
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#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum @8.bias @8.force2
0.000000 -0.8764166537 -0.1653910914 -0.1653910914 -0.8403095298 -0.1425260828 -0.1425260828 -0.5722420612 0.0000000000 0.0000000000
0.050000 -155.2260569032 -42.5600014141 -42.5600014141 -99.5998097725 -4.1424316083 -4.1424316083 -84.9419555586 0.0000000000 0.0000000000
0.100000 -123.1732639577 -34.0261914601 -34.0261914601 -81.0940472347 -3.2850812434 -3.2850812434 -68.0891037308 0.0000000000 0.0000000000
0.150000 -168.5923319466 -47.7585572573 -47.7585572573 -108.5975270667 -4.3920871588 -4.3920871588 -92.3966196711 0.0000000000 0.0000000000
0.200000 -75.5724395563 -2.2688460225 -2.2688460225 -124.2854885655 -45.9215920978 -45.9215920978 -66.6193093739 0.0000000000 0.0000000000
0.250000 -133.6346585875 -4.8852734198 -4.8852734198 -217.8798208143 -83.4591661722 -83.4591661722 -117.1714931339 0.0000000000 0.0000000000
regtest/secondarystructure/rt33-mpi/plumed.dat 0 → 100644
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MOLINFO STRUCTURE=amyloid.pdb
ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=b
ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=brf
ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=br
PARABETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=p
PARABETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=prf
PARABETARMSD RESIDUES=all TYPE=OPTIMAL STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=pr
COMBINE ARG=b.lessthan,p.lessthan PERIODIC=NO LABEL=sum
RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0
DUMPFORCES ARG=* FILE=forces STRIDE=1
PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f
regtest/secondarystructure/rt33/colvar.reference
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#! FIELDS time b.lessthan br.lessthan p.lessthan pr.lessthan sum
0.000000 0.3042 0.1654 0.2681 0.1425 0.5722
0.050000 70.2841 42.5600 14.6579 4.1424 84.9420
0.100000 55.0842 34.0262 13.0049 3.2851 68.0891
0.150000 76.1957 47.7586 16.2009 4.3921 92.3966
0.200000 8.9531 2.2688 57.6662 45.9216 66.6193
0.250000 16.4632 4.8853 100.7083 83.4592 117.1715
#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum
0.000000 0.3042 0.1654 0.1654 0.2681 0.1425 0.1425 0.5722
0.050000 70.2841 42.5600 42.5600 14.6579 4.1424 4.1424 84.9420
0.100000 55.0842 34.0262 34.0262 13.0049 3.2851 3.2851 68.0891
0.150000 76.1957 47.7586 47.7586 16.2009 4.3921 4.3921 92.3966
0.200000 8.9531 2.2688 2.2688 57.6662 45.9216 45.9216 66.6193
0.250000 16.4632 4.8853 4.8853 100.7083 83.4592 83.4592 117.1715
regtest/secondarystructure/rt33/forces.reference 0 → 100644
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#! FIELDS time b.lessthan brf.lessthan br.lessthan p.lessthan prf.lessthan pr.lessthan sum @8.bias @8.force2
0.000000 -0.8764166537 -0.1653910914 -0.1653910914 -0.8403095298 -0.1425260828 -0.1425260828 -0.5722420612 0.0000000000 0.0000000000
0.050000 -155.2260569032 -42.5600014141 -42.5600014141 -99.5998097725 -4.1424316083 -4.1424316083 -84.9419555586 0.0000000000 0.0000000000
0.100000 -123.1732639577 -34.0261914601 -34.0261914601 -81.0940472347 -3.2850812434 -3.2850812434 -68.0891037308 0.0000000000 0.0000000000
0.150000 -168.5923319466 -47.7585572573 -47.7585572573 -108.5975270667 -4.3920871588 -4.3920871588 -92.3966196711 0.0000000000 0.0000000000
0.200000 -75.5724395563 -2.2688460225 -2.2688460225 -124.2854885655 -45.9215920978 -45.9215920978 -66.6193093739 0.0000000000 0.0000000000
0.250000 -133.6346585875 -4.8852734198 -4.8852734198 -217.8798208143 -83.4591661722 -83.4591661722 -117.1714931339 0.0000000000 0.0000000000
regtest/secondarystructure/rt33/plumed.dat
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MOLINFO STRUCTURE=amyloid.pdb
ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=b
ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=br
ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=brf
ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=br
PARABETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=p
PARABETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=pr
PARABETARMSD RESIDUES=all TYPE=OPTIMAL-FAST STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=prf
PARABETARMSD RESIDUES=all TYPE=OPTIMAL STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12 NOSTRETCH} LABEL=pr
COMBINE ARG=b.lessthan,p.lessthan PERIODIC=NO LABEL=sum
PRINT ARG=b.*,br.*,p.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f
RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0
DUMPFORCES ARG=* FILE=forces STRIDE=1
PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f
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