Project ID: plumID:22.004
Source: input_files/Aldol_reaction/1_Discovery/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
UNITSThis command sets the internal units for the code. More detailsLENGTH=A a_1_1:the units of lengthsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=1Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.7The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_2:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_3:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_4:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.7The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_5:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_6:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_7:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.7The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_1_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=1First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_2_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_2the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_2_2:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_3:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_4:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_5:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_6:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_7:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_2_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=2First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_3_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_3the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_3_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_3the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_3_3:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_4:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_5:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_6:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_7:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_3_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=3First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_4_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_4the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_4_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_4the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_4_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_4the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_4_4:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.7The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_5:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_6:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_7:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.7The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_4_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=4First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_5_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_5the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_5_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_5the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_5_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_5the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_5_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_5the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_5_5:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_5_6:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_5_7:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_5_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_5_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_5_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_5_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=5First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_6_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_6the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_6_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_6the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_6_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_6the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_6_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_6the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_6_5:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_5_6the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_6_6:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=6First list of atomsGROUPB=6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_6_7:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=6First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_6_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=6First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_6_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=6First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_6_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=6First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_6_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=6First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_7_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_7the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_7_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_7the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_7_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_7the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_7_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_7the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_7_5:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_5_7the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_7_6:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_6_7the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_7_7:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=7First list of atomsGROUPB=7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_7_8:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=7First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_7_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=7First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_7_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=7First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_7_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=7First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_8_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_5:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_5_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_6:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_6_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_7:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_7_8the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_8_8:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=8First list of atomsGROUPB=8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.7The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_8_9:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=8First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_8_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=8First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_8_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=8First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_9_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_5:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_5_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_6:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_6_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_7:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_7_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_8:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_8_9the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_9_9:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=9First list of atomsGROUPB=9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_9_10:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=9First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_9_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=9First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_10_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_5:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_5_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_6:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_6_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_7:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_7_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_8:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_8_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_9:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_9_10the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_10_10:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=10First list of atomsGROUPB=10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10 a_10_11:The m parameter of the switching function; 0 implies 2*NNCOORDINATIONCalculate coordination numbers. More detailsGROUPA=10First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.2The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
a_11_1:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_1_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_2:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_2_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_3:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_3_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_4:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_4_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_5:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_5_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_6:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_6_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_7:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_7_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_8:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_8_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_9:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_9_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_10:if the output of your function is periodic then you should specify the periodicity of the functionCUSTOMCalculate a combination of variables using a custom expression. More detailsARG=a_10_11the input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO a_11_11:if the output of your function is periodic then you should specify the periodicity of the functionCOORDINATIONCalculate coordination numbers. More detailsGROUPA=11First list of atomsGROUPB=11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.6The r_0 parameter of the switching functionNN=6The n parameter of the switching functionMM=10The m parameter of the switching function; 0 implies 2*NN
cv:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=11_cv.ptFilename of the PyTorch compiled modelARG=a_1_1,a_1_2,a_1_3,a_1_4,a_1_5,a_1_6,a_1_7,a_1_8,a_1_9,a_1_10,a_1_11,a_2_1,a_2_2,a_2_3,a_2_4,a_2_5,a_2_6,a_2_7,a_2_8,a_2_9,a_2_10,a_2_11,a_3_1,a_3_2,a_3_3,a_3_4,a_3_5,a_3_6,a_3_7,a_3_8,a_3_9,a_3_10,a_3_11,a_4_1,a_4_2,a_4_3,a_4_4,a_4_5,a_4_6,a_4_7,a_4_8,a_4_9,a_4_10,a_4_11,a_5_1,a_5_2,a_5_3,a_5_4,a_5_5,a_5_6,a_5_7,a_5_8,a_5_9,a_5_10,a_5_11,a_6_1,a_6_2,a_6_3,a_6_4,a_6_5,a_6_6,a_6_7,a_6_8,a_6_9,a_6_10,a_6_11,a_7_1,a_7_2,a_7_3,a_7_4,a_7_5,a_7_6,a_7_7,a_7_8,a_7_9,a_7_10,a_7_11,a_8_1,a_8_2,a_8_3,a_8_4,a_8_5,a_8_6,a_8_7,a_8_8,a_8_9,a_8_10,a_8_11,a_9_1,a_9_2,a_9_3,a_9_4,a_9_5,a_9_6,a_9_7,a_9_8,a_9_9,a_9_10,a_9_11,a_10_1,a_10_2,a_10_3,a_10_4,a_10_5,a_10_6,a_10_7,a_10_8,a_10_9,a_10_10,a_10_11,a_11_1,a_11_2,a_11_3,a_11_4,a_11_5,a_11_6,a_11_7,a_11_8,a_11_9,a_11_10,a_11_11the input for this action is the scalar output from one or more other actions
#DEFINE WALLS WALLS com1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=1-7 com2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=8-11the list of atoms which are involved the virtual atom's definition
dc1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com2the pair of atom that we are calculating the distance betweenNOPBCignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dc1the arguments on which the bias is actingAT=+5.0the positions of the wallKAPPA=150.0the force constant for the wallEXP=2the powers for the wallsLABEL=uwall_1a label for the action so that its output can be referenced in the input to other actions
opes:OPES_METAD_EXPLORE...On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More detailsARG=cvthe input for this action is the scalar output from one or more other actionsPACE=500the frequency for kernel depositionBARRIER=200the free energy barrier to be overcomeTEMP=300.0 ...temperaturePrint quantities to a file. More detailsARG=cv.*,opes.*,*.biasthe input for this action is the scalar output from one or more other actionsFILE=colvarthe name of the file on which to output these quantitiesSTRIDE=20the frequency with which the quantities of interest should be output