PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:25.003
Source: Alanine_dipeptide/OPES/plumed_all.dat
Originally used with PLUMED version: 2.10
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=input.ala2.pdb
The MOLINFO action with label  calculates somethingphiThe TORSION action with label phi calculates the following quantities: Quantity    Type    Description  
phi scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
psiThe TORSION action with label psi calculates the following quantities: Quantity    Type    Description  
psi scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
eneThe ENERGY action with label ene calculates the following quantities: Quantity    Type    Description  
ene scalar the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,5
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,7
d4The DISTANCE action with label d4 calculates the following quantities: Quantity    Type    Description  
d4 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,9
d5The DISTANCE action with label d5 calculates the following quantities: Quantity    Type    Description  
d5 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,11
d6The DISTANCE action with label d6 calculates the following quantities: Quantity    Type    Description  
d6 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,15
d7The DISTANCE action with label d7 calculates the following quantities: Quantity    Type    Description  
d7 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,16
d8The DISTANCE action with label d8 calculates the following quantities: Quantity    Type    Description  
d8 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,17
d9The DISTANCE action with label d9 calculates the following quantities: Quantity    Type    Description  
d9 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,19
d10The DISTANCE action with label d10 calculates the following quantities: Quantity    Type    Description  
d10 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6
d11The DISTANCE action with label d11 calculates the following quantities: Quantity    Type    Description  
d11 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7
d12The DISTANCE action with label d12 calculates the following quantities: Quantity    Type    Description  
d12 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9
d13The DISTANCE action with label d13 calculates the following quantities: Quantity    Type    Description  
d13 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,11
d14The DISTANCE action with label d14 calculates the following quantities: Quantity    Type    Description  
d14 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,15
d15The DISTANCE action with label d15 calculates the following quantities: Quantity    Type    Description  
d15 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,16
d16The DISTANCE action with label d16 calculates the following quantities: Quantity    Type    Description  
d16 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,17
d17The DISTANCE action with label d17 calculates the following quantities: Quantity    Type    Description  
d17 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,19
d18The DISTANCE action with label d18 calculates the following quantities: Quantity    Type    Description  
d18 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,7
d19The DISTANCE action with label d19 calculates the following quantities: Quantity    Type    Description  
d19 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,9
d20The DISTANCE action with label d20 calculates the following quantities: Quantity    Type    Description  
d20 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,11
d21The DISTANCE action with label d21 calculates the following quantities: Quantity    Type    Description  
d21 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,15
d22The DISTANCE action with label d22 calculates the following quantities: Quantity    Type    Description  
d22 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,16
d23The DISTANCE action with label d23 calculates the following quantities: Quantity    Type    Description  
d23 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,17
d24The DISTANCE action with label d24 calculates the following quantities: Quantity    Type    Description  
d24 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,19
d25The DISTANCE action with label d25 calculates the following quantities: Quantity    Type    Description  
d25 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,9
d26The DISTANCE action with label d26 calculates the following quantities: Quantity    Type    Description  
d26 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,11
d27The DISTANCE action with label d27 calculates the following quantities: Quantity    Type    Description  
d27 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,15
d28The DISTANCE action with label d28 calculates the following quantities: Quantity    Type    Description  
d28 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,16
d29The DISTANCE action with label d29 calculates the following quantities: Quantity    Type    Description  
d29 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,17
d30The DISTANCE action with label d30 calculates the following quantities: Quantity    Type    Description  
d30 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,19
d31The DISTANCE action with label d31 calculates the following quantities: Quantity    Type    Description  
d31 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,11
d32The DISTANCE action with label d32 calculates the following quantities: Quantity    Type    Description  
d32 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,15
d33The DISTANCE action with label d33 calculates the following quantities: Quantity    Type    Description  
d33 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,16
d34The DISTANCE action with label d34 calculates the following quantities: Quantity    Type    Description  
d34 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,17
d35The DISTANCE action with label d35 calculates the following quantities: Quantity    Type    Description  
d35 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,19
d36The DISTANCE action with label d36 calculates the following quantities: Quantity    Type    Description  
d36 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,15
d37The DISTANCE action with label d37 calculates the following quantities: Quantity    Type    Description  
d37 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,16
d38The DISTANCE action with label d38 calculates the following quantities: Quantity    Type    Description  
d38 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,17
d39The DISTANCE action with label d39 calculates the following quantities: Quantity    Type    Description  
d39 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,19
d40The DISTANCE action with label d40 calculates the following quantities: Quantity    Type    Description  
d40 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,16
d41The DISTANCE action with label d41 calculates the following quantities: Quantity    Type    Description  
d41 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,17
d42The DISTANCE action with label d42 calculates the following quantities: Quantity    Type    Description  
d42 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,19
d43The DISTANCE action with label d43 calculates the following quantities: Quantity    Type    Description  
d43 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,17
d44The DISTANCE action with label d44 calculates the following quantities: Quantity    Type    Description  
d44 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,19
d45The DISTANCE action with label d45 calculates the following quantities: Quantity    Type    Description  
d45 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,19

t1The TORSION action with label t1 calculates the following quantities: Quantity    Type    Description  
t1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
t2The TORSION action with label t2 calculates the following quantities: Quantity    Type    Description  
t2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
t3The TORSION action with label t3 calculates the following quantities: Quantity    Type    Description  
t3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,5,6
t4The TORSION action with label t4 calculates the following quantities: Quantity    Type    Description  
t4 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,5,7
t5The TORSION action with label t5 calculates the following quantities: Quantity    Type    Description  
t5 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,2,5,6
t6The TORSION action with label t6 calculates the following quantities: Quantity    Type    Description  
t6 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,2,5,7
t7The TORSION action with label t7 calculates the following quantities: Quantity    Type    Description  
t7 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,2,5,6
t8The TORSION action with label t8 calculates the following quantities: Quantity    Type    Description  
t8 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,2,5,7
t9The TORSION action with label t9 calculates the following quantities: Quantity    Type    Description  
t9 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,5,7,8
t10The TORSION action with label t10 calculates the following quantities: Quantity    Type    Description  
t10 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,5,7,9
t11The TORSION action with label t11 calculates the following quantities: Quantity    Type    Description  
t11 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=6,5,7,8
t12The TORSION action with label t12 calculates the following quantities: Quantity    Type    Description  
t12 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2,5,7,9
t13The TORSION action with label t13 calculates the following quantities: Quantity    Type    Description  
t13 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,10
t14The TORSION action with label t14 calculates the following quantities: Quantity    Type    Description  
t14 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,11
t15The TORSION action with label t15 calculates the following quantities: Quantity    Type    Description  
t15 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=8,7,9,10
t16The TORSION action with label t16 calculates the following quantities: Quantity    Type    Description  
t16 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=8,7,9,11
t17The TORSION action with label t17 calculates the following quantities: Quantity    Type    Description  
t17 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=8,7,9,15
t18The TORSION action with label t18 calculates the following quantities: Quantity    Type    Description  
t18 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,11,12
t19The TORSION action with label t19 calculates the following quantities: Quantity    Type    Description  
t19 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,11,13
t20The TORSION action with label t20 calculates the following quantities: Quantity    Type    Description  
t20 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,11,14
t21The TORSION action with label t21 calculates the following quantities: Quantity    Type    Description  
t21 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=10,9,11,12
t22The TORSION action with label t22 calculates the following quantities: Quantity    Type    Description  
t22 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=10,9,11,13
t23The TORSION action with label t23 calculates the following quantities: Quantity    Type    Description  
t23 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=10,9,11,14
t24The TORSION action with label t24 calculates the following quantities: Quantity    Type    Description  
t24 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,9,11,12
t25The TORSION action with label t25 calculates the following quantities: Quantity    Type    Description  
t25 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,9,11,13
t26The TORSION action with label t26 calculates the following quantities: Quantity    Type    Description  
t26 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,9,11,14
t27The TORSION action with label t27 calculates the following quantities: Quantity    Type    Description  
t27 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,16
t28The TORSION action with label t28 calculates the following quantities: Quantity    Type    Description  
t28 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=10,9,15,16
t29The TORSION action with label t29 calculates the following quantities: Quantity    Type    Description  
t29 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=10,9,15,17
t30The TORSION action with label t30 calculates the following quantities: Quantity    Type    Description  
t30 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=11,9,15,16
t31The TORSION action with label t31 calculates the following quantities: Quantity    Type    Description  
t31 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=11,9,15,17
t32The TORSION action with label t32 calculates the following quantities: Quantity    Type    Description  
t32 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=9,15,17,18
t33The TORSION action with label t33 calculates the following quantities: Quantity    Type    Description  
t33 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=9,15,17,19
t34The TORSION action with label t34 calculates the following quantities: Quantity    Type    Description  
t34 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16,15,17,18
t35The TORSION action with label t35 calculates the following quantities: Quantity    Type    Description  
t35 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=16,15,17,19
t36The TORSION action with label t36 calculates the following quantities: Quantity    Type    Description  
t36 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,20
t37The TORSION action with label t37 calculates the following quantities: Quantity    Type    Description  
t37 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,21
t38The TORSION action with label t38 calculates the following quantities: Quantity    Type    Description  
t38 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,22
t39The TORSION action with label t39 calculates the following quantities: Quantity    Type    Description  
t39 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=18,17,19,20
 
cost1The MATHEVAL action with label cost1 calculates the following quantities: Quantity    Type    Description  
cost1 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t1 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost2The MATHEVAL action with label cost2 calculates the following quantities: Quantity    Type    Description  
cost2 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t2 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost3The MATHEVAL action with label cost3 calculates the following quantities: Quantity    Type    Description  
cost3 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t3 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost4The MATHEVAL action with label cost4 calculates the following quantities: Quantity    Type    Description  
cost4 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t4 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost5The MATHEVAL action with label cost5 calculates the following quantities: Quantity    Type    Description  
cost5 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t5 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost6The MATHEVAL action with label cost6 calculates the following quantities: Quantity    Type    Description  
cost6 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t6 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost7The MATHEVAL action with label cost7 calculates the following quantities: Quantity    Type    Description  
cost7 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t7 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost8The MATHEVAL action with label cost8 calculates the following quantities: Quantity    Type    Description  
cost8 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t8 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost9The MATHEVAL action with label cost9 calculates the following quantities: Quantity    Type    Description  
cost9 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t9 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost10The MATHEVAL action with label cost10 calculates the following quantities: Quantity    Type    Description  
cost10 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t10 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost11The MATHEVAL action with label cost11 calculates the following quantities: Quantity    Type    Description  
cost11 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t11 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost12The MATHEVAL action with label cost12 calculates the following quantities: Quantity    Type    Description  
cost12 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t12 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost13The MATHEVAL action with label cost13 calculates the following quantities: Quantity    Type    Description  
cost13 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t13 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost14The MATHEVAL action with label cost14 calculates the following quantities: Quantity    Type    Description  
cost14 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t14 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost15The MATHEVAL action with label cost15 calculates the following quantities: Quantity    Type    Description  
cost15 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t15 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost16The MATHEVAL action with label cost16 calculates the following quantities: Quantity    Type    Description  
cost16 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t16 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost17The MATHEVAL action with label cost17 calculates the following quantities: Quantity    Type    Description  
cost17 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t17 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost18The MATHEVAL action with label cost18 calculates the following quantities: Quantity    Type    Description  
cost18 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t18 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost19The MATHEVAL action with label cost19 calculates the following quantities: Quantity    Type    Description  
cost19 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t19 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost20The MATHEVAL action with label cost20 calculates the following quantities: Quantity    Type    Description  
cost20 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t20 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost21The MATHEVAL action with label cost21 calculates the following quantities: Quantity    Type    Description  
cost21 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t21 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost22The MATHEVAL action with label cost22 calculates the following quantities: Quantity    Type    Description  
cost22 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t22 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost23The MATHEVAL action with label cost23 calculates the following quantities: Quantity    Type    Description  
cost23 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t23 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost24The MATHEVAL action with label cost24 calculates the following quantities: Quantity    Type    Description  
cost24 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t24 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost25The MATHEVAL action with label cost25 calculates the following quantities: Quantity    Type    Description  
cost25 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t25 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost26The MATHEVAL action with label cost26 calculates the following quantities: Quantity    Type    Description  
cost26 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t26 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost27The MATHEVAL action with label cost27 calculates the following quantities: Quantity    Type    Description  
cost27 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t27 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost28The MATHEVAL action with label cost28 calculates the following quantities: Quantity    Type    Description  
cost28 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t28 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost29The MATHEVAL action with label cost29 calculates the following quantities: Quantity    Type    Description  
cost29 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t29 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost30The MATHEVAL action with label cost30 calculates the following quantities: Quantity    Type    Description  
cost30 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t30 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost31The MATHEVAL action with label cost31 calculates the following quantities: Quantity    Type    Description  
cost31 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t31 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost32The MATHEVAL action with label cost32 calculates the following quantities: Quantity    Type    Description  
cost32 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t32 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost33The MATHEVAL action with label cost33 calculates the following quantities: Quantity    Type    Description  
cost33 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t33 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost34The MATHEVAL action with label cost34 calculates the following quantities: Quantity    Type    Description  
cost34 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t34 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost35The MATHEVAL action with label cost35 calculates the following quantities: Quantity    Type    Description  
cost35 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t35 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost36The MATHEVAL action with label cost36 calculates the following quantities: Quantity    Type    Description  
cost36 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t36 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost37The MATHEVAL action with label cost37 calculates the following quantities: Quantity    Type    Description  
cost37 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t37 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost38The MATHEVAL action with label cost38 calculates the following quantities: Quantity    Type    Description  
cost38 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t38 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cost39The MATHEVAL action with label cost39 calculates the following quantities: Quantity    Type    Description  
cost39 scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=t39 FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Deep-TDA CV (distances as descriptor)
deepTDAThe PYTORCH_MODEL action with label deepTDA calculates the following quantities: Quantity    Type    Description  
deepTDA.node-0 scalar Model outputs  This is the 0th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=ala2_deepTDA.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#Surrogate Model of Deep-TDA CV (distances as descriptor)
lassoTDAThe COMBINE action with label lassoTDA calculates the following quantities: Quantity    Type    Description  
lassoTDA scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d9,d19,d20,d21,d22,d23,d24,d25,d26,d28,d30,d33,d37,d38,d39, COEFFICIENTS the coefficients of the arguments in your function=4.2236,123.9035,-74.1519,-24.5484,-20.8633,-3.6156,-10.3116,-15.1608,36.7252,22.8718,8.6337,-1.8104,5.3758,-1.7865,-0.6806, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 
lassoCV_TDAThe MATHEVAL action with label lassoCV_TDA calculates the following quantities: Quantity    Type    Description  
lassoCV_TDA scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lassoTDA FUNCthe function you wish to evaluate=x-6.1677 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


#Deep-TICA CV (distances as descriptor)
deepTICAThe PYTORCH_MODEL action with label deepTICA calculates the following quantities: Quantity    Type    Description  
deepTICA.node-0 scalar Model outputs  This is the 0th of these quantities
deepTICA.node-1 scalar Model outputs  This is the 1th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=ala2_deepTICA.ptc ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#Surrogate Model of Deep-TICA CV (distances as descriptor)
lassoTICAThe COMBINE action with label lassoTICA calculates the following quantities: Quantity    Type    Description  
lassoTICA scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d3,d5,d9,d11,d13,d16,d17,d19,d20,d21,d22,d23,d26,d27,d28,d30,d33,d34,d37,d38,d43,d44, COEFFICIENTS the coefficients of the arguments in your function=-2.1943,0.5962,0.2754,-0.4293,-0.7594,-0.1269,-1.7356,13.3339,-8.7770,-0.1922,-2.5192,-2.5143,3.1540,1.5354,1.8088,2.4623,-1.7945,0.2039,1.0735,-0.0421,-1.9173,-0.0261, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 
lassoCV_TICAThe MATHEVAL action with label lassoCV_TICA calculates the following quantities: Quantity    Type    Description  
lassoCV_TICA scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lassoTICA FUNCthe function you wish to evaluate=x+0.1539 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Deep-TDA CV (torsion angles as descriptor)
deepTDA_torsionThe PYTORCH_MODEL action with label deepTDA_torsion calculates the following quantities: Quantity    Type    Description  
deepTDA_torsion.node-0 scalar Model outputs  This is the 0th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=ala2_torsion_deepTDA.pt ARGthe labels of the values from which the function is calculated=cost1,cost2,cost3,cost4,cost5,cost6,cost7,cost8,cost9,cost10,cost11,cost12,cost13,cost14,cost15,cost16,cost17,cost18,cost19,cost20,cost21,cost22,cost23,cost24,cost25,cost26,cost27,cost28,cost29,cost30,cost31,cost32,cost33,cost34,cost35,cost36,cost37,cost38,cost39

#Surrogate Model of Deep-TDA CV ( torsion angles as descriptor)
lassoTDA_torsionThe COMBINE action with label lassoTDA_torsion calculates the following quantities: Quantity    Type    Description  
lassoTDA_torsion scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cost1,cost4,cost10,cost11,cost12,cost14,cost15,cost16,cost17,cost18,cost20,cost27,cost30,cost31,cost34,cost37,cost38, COEFFICIENTS the coefficients of the arguments in your function=4.1663,0.0186,-0.0581,-0.1556,-0.0001,-0.2719,0.5317,0.6360,-0.3828,0.0069,-0.0240,0.0418,-0.1093,0.0003,0.0484,-0.0143,0.0014, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 
lassoCV_TDA_torsionThe MATHEVAL action with label lassoCV_TDA_torsion calculates the following quantities: Quantity    Type    Description  
lassoCV_TDA_torsion scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lassoTDA_torsion FUNCthe function you wish to evaluate=x-2.6641 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO





OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opesThe OPES_METAD action with label opes calculates the following quantities: Quantity    Type    Description  
opes.bias scalar the instantaneous value of the bias potential
opes.rct scalar estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed scalar estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff scalar effective sample size
opes.nker scalar total number of compressed kernels used to represent the bias
  ARGthe labels of the scalars on which the bias will act=deepTDA.node-0
  #ARG=lassoCV_TDA
  #ARG=deepTICA.node-0
  #ARG=lassoCV_TICA
  #ARG=deepTDA_torsion.node-0
  #ARG=lassoCV_TDA_torsion
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=40
  TEMP temperature=300
...
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=deepTDA.node-0
  #ARG=lassoCV_TDA
  #ARG=deepTICA.node-0
  #ARG=lassoCV_TICA
  #ARG=deepTDA_torsion.node-0
  #ARG=lassoCV_TDA_torsion
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=40
  TEMP temperature=300
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...


PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=deepTDA.node-0,lassoCV_TDA,deepTICA.node-0,lassoCV_TICA,deepTDA_torsion.node-0,lassoCV_TDA_torsion,opes.bias

ENDPLUMEDTerminate plumed input. More details
Quantity	Type	Description
phi	scalar	the TORSION involving these atoms
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
