Project ID: plumID:21.008
Source: REM-FEP/replica009/plumed.dat
Originally used with PLUMED version: 2.7
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
tested onv2.10
tested onmaster
RESTARTActivate restart. More details
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-347




TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=4,3,84,85    LABELa label for the action so that its output can be referenced in the input to other actions=T1   
TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=74,73,153,154  LABELa label for the action so that its output can be referenced in the input to other actions=T2
TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=143,142,222,223 LABELa label for the action so that its output can be referenced in the input to other actions=T3
TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=212,211,280,293  LABELa label for the action so that its output can be referenced in the input to other actions=T4     


# this the lambda value for current window lambda1: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=0.32 lambda2: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=0.00


# first we define V0 for T1 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V0_1 ARGthe values input to this function=T1 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V1 for T1 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V1_1 ARGthe values input to this function=T1 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=301.3-0.1478*cos(x-pi)-48.16*(cos(x-pi))^2+0.9948*(cos(x-pi))^3+34.30*(cos(x-pi))^4-1.001*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V2 for T1 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V2_1 ARGthe values input to this function=T1 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=348.8-0.1104*cos(x-pi)-54.71*(cos(x-pi))^2+0.7533*(cos(x-pi))^3+35.14*(cos(x-pi))^4-0.8068*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# first we define V0 for T2 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V0_2 ARGthe values input to this function=T2 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V1 for T2 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V1_2 ARGthe values input to this function=T2 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=313.9+0.3972*cos(x-pi)-72.12*(cos(x-pi))^2-0.9463*(cos(x-pi))^3+43.87*(cos(x-pi))^4+0.5858*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V2 for T2 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V2_2 ARGthe values input to this function=T2 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=351.9-0.7135*cos(x-pi)-69.01*(cos(x-pi))^2+0.653*(cos(x-pi))^3+47.11*(cos(x-pi))^4+0.41*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# first we define V0 for T3 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V0_3 ARGthe values input to this function=T3 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V1 for T3 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V1_3 ARGthe values input to this function=T3 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=313.9+0.3972*cos(x-pi)-72.12*(cos(x-pi))^2-0.9463*(cos(x-pi))^3+43.87*(cos(x-pi))^4+0.5858*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V2 for T3 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V2_3 ARGthe values input to this function=T3 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=351.9-0.7135*cos(x-pi)-69.01*(cos(x-pi))^2+0.653*(cos(x-pi))^3+47.11*(cos(x-pi))^4+0.41*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# first we define V0 for T4
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V0_4 ARGthe values input to this function=T4 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=12.16-0.024*cos(x-pi)-43.32*(cos(x-pi))^2+0.12*(cos(x-pi))^3+38.8*(cos(x-pi))^4-0.0601*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V1 for T4 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V1_4 ARGthe values input to this function=T4 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=301.3-0.1478*cos(x-pi)-48.16*(cos(x-pi))^2+0.9948*(cos(x-pi))^3+34.30*(cos(x-pi))^4-1.001*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# then V2 for T4 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=V2_4 ARGthe values input to this function=T4 VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=348.8-0.1104*cos(x-pi)-54.71*(cos(x-pi))^2+0.7533*(cos(x-pi))^3+35.14*(cos(x-pi))^4-0.8068*(cos(x-pi))^5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
# This is Vlambda1 for current window Vlambda1: 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=V0_1,V1_1,V2_1,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1)*x+l1*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdam1: 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=V0_1,V1_1,V2_1,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdap1: 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=V0_1,V1_1,V2_1,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlbias1: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=Vlambda1 # This is Vlambda2 for current window Vlambda2: 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=V0_2,V1_2,V2_2,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1)*x+l1*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdam2: 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=V0_2,V1_2,V2_2,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdap2: 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=V0_2,V1_2,V2_2,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlbias2: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=Vlambda2 # This is Vlambda3 for current window Vlambda3: 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=V0_3,V1_3,V2_3,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1)*x+l1*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdam3: 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=V0_3,V1_3,V2_3,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdap3: 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=V0_3,V1_3,V2_3,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlbias3: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=Vlambda3 # This is Vlambda4 for current window Vlambda4: 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=V0_4,V1_4,V2_4,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1)*x+l1*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdam4: 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=V0_4,V1_4,V2_4,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1+0.04)*x+(l1-0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlambdap4: 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=V0_4,V1_4,V2_4,lambda1,lambda2 VARthe names to give each of the arguments in the function=x,y,z,l1,l2 FUNCthe function you wish to evaluate=(1.0-l1-0.04)*x+(l1+0.04)*(1-l2)*y+l2*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO Vlbias4: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=Vlambda4 PBMETADUsed to performed Parallel Bias metadynamics. More details ... ARGthe labels of the scalars on which the bias will act=T1,T2,T3,T4 SIGMAthe widths of the Gaussian hills=0.2,0.2,0.2,0.2 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 PACEthe frequency for hill addition, one for all biases=500 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=40 LABELa label for the action so that its output can be referenced in the input to other actions=pb FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_T1,HILLS_T2,HILLS_T3,HILLS_T4 ... PBMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=T1,T2,T3,T4,Vlambdam1,Vlambda1,Vlambdap1,Vlambdam2,Vlambda2,Vlambdap2,Vlambdam3,Vlambda3,Vlambdap3,Vlambdam4,Vlambda4,Vlambdap4,pb.bias 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