diff --git a/test/amber/.gitignore b/test/amber/.gitignore deleted file mode 100644 index e12bdc2ee6..0000000000 --- a/test/amber/.gitignore +++ /dev/null @@ -1,6 +0,0 @@ -* -!amber_input -!system.inpcrd -!system.prmtop -!plumed.dat -!.gitignore diff --git a/test/amber/amber_input b/test/amber/amber_input deleted file mode 100644 index fe7da236d9..0000000000 --- a/test/amber/amber_input +++ /dev/null @@ -1,11 +0,0 @@ -METADYNAMICS TEST -&cntrl - imin=0, irest=0, ntx=1, ig=71278 , - nstlim=1001, dt=0.0002, - ntc=1, ntf=1, - ntt=3, gamma_ln=5 , - tempi=300.0, temp0=300.0, - ntpr=200, ntwx=0, - ntb=0, igb=0, - cut=999., plumed=1 , plumedfile='plumed.dat' -/ diff --git a/test/amber/plumed.dat b/test/amber/plumed.dat deleted file mode 100644 index c0be884454..0000000000 --- a/test/amber/plumed.dat +++ /dev/null @@ -1,4 +0,0 @@ -DISTANCE ATOMS=0,10 LABEL=dist -ENERGY -RESTRAINT ARG=dist KAPPA=10000 AT=0.3 -PRINT ARG=* FILE=COLVAR diff --git a/test/amber/system.inpcrd b/test/amber/system.inpcrd deleted file mode 100644 index b732823e35..0000000000 --- a/test/amber/system.inpcrd +++ /dev/null @@ -1,13 +0,0 @@ -ACE - 22 - 2.0177833 1.0353295 0.0542168 1.9998067 2.1250666 0.0538082 - 1.4254166 2.4843904 0.9072400 1.5326313 2.4823206 -0.8638698 - 3.4222907 2.6597886 0.1389017 4.3607216 1.8984493 0.3631598 - 3.5879191 3.9603571 -0.1138393 2.7859198 4.5436605 -0.3046603 - 4.8919526 4.5905945 -0.0675145 5.4432975 4.2337999 0.8026422 - 5.6616692 4.2349396 -1.3354247 5.1089564 4.5854833 -2.2068147 - 6.6419078 4.7111339 -1.3103306 5.7851258 3.1535202 -1.3931851 - 4.7222411 6.1004128 0.0215211 3.6035082 6.6057631 -0.0398724 - 5.8431179 6.8242650 0.0735169 6.7415384 6.3635968 0.0875836 - 5.8209701 8.2733497 0.0569928 4.7879086 8.6215931 0.0518138 - 6.3303031 8.6556759 0.9417330 6.3290771 8.6329497 -0.8383083 diff --git a/test/amber/system.prmtop b/test/amber/system.prmtop deleted file mode 100644 index 702853ce1c..0000000000 --- a/test/amber/system.prmtop +++ /dev/null @@ -1,232 +0,0 @@ -%VERSION VERSION_STAMP = V0001.000 DATE = 05/31/08 11:43:33 -%FLAG TITLE -%FORMAT(20a4) -ACE -%FLAG POINTERS -%FORMAT(10I8) - 22 7 12 9 25 11 42 24 0 0 - 99 3 9 11 24 8 16 19 7 0 - 0 0 0 0 0 0 0 0 10 0 - 0 -%FLAG ATOM_NAME -%FORMAT(20a4) -HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31 -HH32HH33 -%FLAG CHARGE -%FORMAT(5E16.8) - 2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01 - -1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00 - -3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01 - -1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00 - 1.77849648E+00 1.77849648E+00 -%FLAG MASS -%FORMAT(5E16.8) - 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01 - 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 - 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01 - 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 - 1.00800000E+00 1.00800000E+00 -%FLAG ATOM_TYPE_INDEX -%FORMAT(10I8) - 1 2 1 1 3 4 5 6 2 7 - 2 1 1 1 3 4 5 6 2 7 - 7 7 -%FLAG NUMBER_EXCLUDED_ATOMS -%FORMAT(10I8) - 6 7 4 3 7 3 10 4 10 7 - 6 3 2 1 7 3 5 4 3 2 - 1 1 -%FLAG NONBONDED_PARM_INDEX -%FORMAT(10I8) - 1 2 4 7 11 16 22 2 3 5 - 8 12 17 23 4 5 6 9 13 18 - 24 7 8 9 10 14 19 25 11 12 - 13 14 15 20 26 16 17 18 19 20 - 21 27 22 23 24 25 26 27 28 -%FLAG RESIDUE_LABEL -%FORMAT(20a4) -ACE ALA NME -%FLAG RESIDUE_POINTER -%FORMAT(10I8) - 1 7 17 -%FLAG BOND_FORCE_CONSTANT -%FORMAT(5E16.8) - 5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02 - 3.10000000E+02 4.34000000E+02 3.37000000E+02 -%FLAG BOND_EQUIL_VALUE -%FORMAT(5E16.8) - 1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00 - 1.52600000E+00 1.01000000E+00 1.44900000E+00 -%FLAG ANGLE_FORCE_CONSTANT -%FORMAT(5E16.8) - 8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01 - 8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01 - 5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01 - 3.50000000E+01 -%FLAG ANGLE_EQUIL_VALUE -%FORMAT(5E16.8) - 2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00 - 2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00 - 1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00 - 1.91113635E+00 -%FLAG DIHEDRAL_FORCE_CONSTANT -%FORMAT(5E16.8) - 2.00000000E+00 2.50000000E+00 0.00000000E+00 2.00000000E+00 4.00000000E-01 - 0.00000000E+00 0.00000000E+00 2.70000000E-01 4.20000000E-01 8.00000000E-01 - 8.00000000E-02 1.55555556E-01 2.00000000E-01 2.00000000E-01 4.50000000E-01 - 1.58000000E+00 5.50000000E-01 1.05000000E+01 1.10000000E+00 -%FLAG DIHEDRAL_PERIODICITY -%FORMAT(5E16.8) - 1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00 - 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 - 3.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00 1.00000000E+00 - 2.00000000E+00 3.00000000E+00 2.00000000E+00 2.00000000E+00 -%FLAG DIHEDRAL_PHASE -%FORMAT(5E16.8) - 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 - 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 -%FLAG SOLTY -%FORMAT(5E16.8) - 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 - 0.00000000E+00 0.00000000E+00 -%FLAG LENNARD_JONES_ACOEF -%FORMAT(5E16.8) - 7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05 - 8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05 - 8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05 - 1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03 - 1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04 - 6.20665997E+04 5.94667300E+01 3.25969625E+03 -%FLAG LENNARD_JONES_BCOEF -%FORMAT(5E16.8) - 2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02 - 5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02 - 1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02 - 2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01 - 9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01 - 1.13252061E+02 1.93248820E+00 1.43076527E+01 -%FLAG BONDS_INC_HYDROGEN -%FORMAT(10I8) - 3 6 3 3 9 3 0 3 3 30 - 33 3 30 36 3 30 39 3 24 27 - 5 18 21 7 54 57 5 54 60 5 - 54 63 5 48 51 7 -%FLAG BONDS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 12 15 1 12 18 2 3 12 4 42 - 45 1 42 48 2 24 30 6 24 42 - 4 18 24 8 48 54 8 -%FLAG ANGLES_INC_HYDROGEN -%FORMAT(10I8) - 12 18 21 2 9 3 12 4 6 3 - 9 5 6 3 12 4 0 3 6 5 - 0 3 9 5 0 3 12 4 42 48 - 51 2 36 30 39 5 33 30 36 5 - 33 30 39 5 27 24 30 9 27 24 - 42 10 24 30 33 11 24 30 36 11 - 24 30 39 11 21 18 24 12 18 24 - 27 13 60 54 63 16 57 54 60 16 - 57 54 63 16 51 48 54 12 48 54 - 57 13 48 54 60 13 48 54 63 13 -%FLAG ANGLES_WITHOUT_HYDROGEN -%FORMAT(10I8) - 15 12 18 1 12 18 24 3 3 12 - 15 6 3 12 18 7 45 42 48 1 - 42 48 54 3 30 24 42 8 24 42 - 45 6 24 42 48 7 18 24 30 14 - 18 24 42 15 -%FLAG DIHEDRALS_INC_HYDROGEN -%FORMAT(10I8) - 15 12 18 21 1 15 12 -18 21 2 - 12 18 24 27 3 9 3 12 15 10 - 9 3 -12 15 3 9 3 -12 15 11 - 9 3 12 18 3 6 3 12 15 10 - 6 3 -12 15 3 6 3 -12 15 11 - 6 3 12 18 3 3 12 18 21 2 - 0 3 12 15 10 0 3 -12 15 3 - 0 3 -12 15 11 0 3 12 18 3 - 45 42 48 51 1 45 42 -48 51 2 - 42 48 54 57 3 42 48 54 60 3 - 42 48 54 63 3 39 30 24 42 12 - 36 30 24 42 12 33 30 24 42 12 - 27 24 30 33 12 27 24 30 36 12 - 27 24 30 39 12 27 24 42 45 10 - 27 24 -42 45 11 27 24 42 48 3 - 24 42 48 51 2 21 18 24 27 3 - 21 18 24 30 3 21 18 24 42 3 - 18 24 30 33 12 18 24 30 36 12 - 18 24 30 39 12 51 48 54 57 3 - 51 48 54 60 3 51 48 54 63 3 - 12 24 -18 -21 19 42 54 -48 -51 19 -%FLAG DIHEDRALS_WITHOUT_HYDROGEN -%FORMAT(10I8) - 15 12 18 24 2 12 18 24 30 1 - 12 18 -24 30 4 12 18 -24 30 5 - 12 18 -24 30 6 12 18 24 42 7 - 12 18 -24 42 8 12 18 -24 42 9 - 12 18 -24 42 6 3 12 18 24 2 - 45 42 48 54 2 30 24 42 45 3 - 30 24 42 48 13 30 24 -42 48 14 - 30 24 -42 48 5 30 24 -42 48 6 - 24 42 48 54 2 18 24 42 45 3 - 18 24 42 48 15 18 24 -42 48 16 - 18 24 -42 48 17 18 24 -42 48 6 - 3 18 -12 -15 18 24 48 -42 -45 18 -%FLAG EXCLUDED_ATOMS_LIST -%FORMAT(10I8) - 2 3 4 5 6 7 3 4 5 6 - 7 8 9 4 5 6 7 5 6 7 - 6 7 8 9 10 11 15 7 8 9 - 8 9 10 11 12 13 14 15 16 17 - 9 10 11 15 10 11 12 13 14 15 - 16 17 18 19 11 12 13 14 15 16 - 17 12 13 14 15 16 17 13 14 15 - 14 15 15 16 17 18 19 20 21 22 - 17 18 19 18 19 20 21 22 19 20 - 21 22 20 21 22 21 22 22 0 -%FLAG HBOND_ACOEF -%FORMAT(5E16.8) - -%FLAG HBOND_BCOEF -%FORMAT(5E16.8) - -%FLAG HBCUT -%FORMAT(5E16.8) - -%FLAG AMBER_ATOM_TYPE -%FORMAT(20a4) -HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1 -H1 H1 -%FLAG TREE_CHAIN_CLASSIFICATION -%FORMAT(20a4) -M M E E M E M E M E 3 E E E M E M E M E -E E -%FLAG JOIN_ARRAY -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 0 - 0 0 -%FLAG IROTAT -%FORMAT(10I8) - 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 0 0 - 0 0 -%FLAG RADIUS_SET -%FORMAT(1a80) -modified Bondi radii (mbondi) -%FLAG RADII -%FORMAT(5E16.8) - 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 - 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 - 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 - 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 - 1.30000000E+00 1.30000000E+00 -%FLAG SCREEN -%FORMAT(5E16.8) - 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 - 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 - 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 - 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 - 8.50000000E-01 8.50000000E-01 diff --git a/test/gromacs/plumed.dat b/test/gromacs/plumed.dat index b92eda9ba0..fbe2822233 100644 --- a/test/gromacs/plumed.dat +++ b/test/gromacs/plumed.dat @@ -1,4 +1,3 @@ -LOAD ../../extensions/libplumedExtensions.dylib c: DISTANCE ATOMS=1,10 PRINT ARG=c FILE=ooo METAD ARG=c SIGMA=0.1 HEIGHT=1.0 PACE=10 RESTART diff --git a/test/namd/plumed.dat b/test/namd/plumed.dat index d21247cc8f..93b8191229 100644 --- a/test/namd/plumed.dat +++ b/test/namd/plumed.dat @@ -1,30 +1,6 @@ -DISTANCE ATOMS=0,21 LABEL=C1 COMPONENTS -VOLUME LABEL=vol -ENERGY LABEL=ene +c1: DISTANCE ATOMS=1,10 -COMBINE LABEL=x ARG=C1.x,C1.y,C1.z POWERS=2,2,2 -COMBINE LABEL=xx ARG=x POWERS=0.5 - -#RESTRAINT ARG=C1 AT=1.1 KAPPA=10000.0 - -#MOVINGRESTRAINT ARG=ene AT0=-8525.08 KAPPA0=0.024 AT1=-8000 STEP0=0 STEP1=10000 -#RESTRAINT ARG=ene AT=-8525.08 KAPPA=-0.0002 STRIDE=2 - -RESTRAINT ARG=C1 AT=0.4 KAPPA=1000.0 - -#RESTRAINT ARG=vol AT=6.8 KAPPA=100.0 - -FLUSH STRIDE=100 - -PRINT ARG=C1,vol,ene,C1.x,C1.y,C1.z STRIDE=1 FILE=COLVAR - -##PRINT ... -## ARG=*.* -## STRIDE=10 -## FILE=COLVAR_ALL -##... PRINT - -DEBUG logActivity +PRINT ARG=c1 ENDPLUMED