Project ID: plumID:19.019
Source: FA-MetaD-Ala3-plumed/plumed_FaMetaD.dat
Originally used with PLUMED version: 2.5
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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=GMXfiles/ala3.pdb
The MOLINFO action with label calculates somethingFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1
ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c1The ALPHABETA action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=@phi-2 REFERENCE=1.25 LABEL=c1
c1_torsionsThe TORSION action with label c1_torsions calculates the following quantities:| Quantity | Type | Description |
| c1_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the 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.
c1_refThe CONSTANT action with label c1_ref calculates the following quantities:| Quantity | Type | Description |
| c1_ref | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.25
c1_coeffThe CONSTANT action with label c1_coeff calculates the following quantities:| Quantity | Type | Description |
| c1_coeff | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1
c1_combThe COMBINE action with label c1_comb calculates the following quantities:| Quantity | Type | Description |
| c1_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c1_torsions,c1_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c1_cosThe CUSTOM action with label c1_cos calculates the following quantities:| Quantity | Type | Description |
| c1_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c1_comb,c1_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c1The SUM action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c1_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c3The ALPHABETA action with label c3 calculates the following quantities:| Quantity | Type | Description |
| c3 | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=@phi-3 REFERENCE=1.25 LABEL=c3
c3_torsionsThe TORSION action with label c3_torsions calculates the following quantities:| Quantity | Type | Description |
| c3_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.
c3_refThe CONSTANT action with label c3_ref calculates the following quantities:| Quantity | Type | Description |
| c3_ref | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.25
c3_coeffThe CONSTANT action with label c3_coeff calculates the following quantities:| Quantity | Type | Description |
| c3_coeff | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1
c3_combThe COMBINE action with label c3_comb calculates the following quantities:| Quantity | Type | Description |
| c3_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c3_torsions,c3_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c3_cosThe CUSTOM action with label c3_cos calculates the following quantities:| Quantity | Type | Description |
| c3_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c3_comb,c3_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c3The SUM action with label c3 calculates the following quantities:| Quantity | Type | Description |
| c3 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c3_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c5The ALPHABETA action with label c5 calculates the following quantities:| Quantity | Type | Description |
| c5 | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=@phi-4 REFERENCE=1.25 LABEL=c5
c5_torsionsThe TORSION action with label c5_torsions calculates the following quantities:| Quantity | Type | Description |
| c5_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.
c5_refThe CONSTANT action with label c5_ref calculates the following quantities:| Quantity | Type | Description |
| c5_ref | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.25
c5_coeffThe CONSTANT action with label c5_coeff calculates the following quantities:| Quantity | Type | Description |
| c5_coeff | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1
c5_combThe COMBINE action with label c5_comb calculates the following quantities:| Quantity | Type | Description |
| c5_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c5_torsions,c5_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c5_cosThe CUSTOM action with label c5_cos calculates the following quantities:| Quantity | Type | Description |
| c5_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c5_comb,c5_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c5The SUM action with label c5 calculates the following quantities:| Quantity | Type | Description |
| c5 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c5_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c2The ALPHABETA action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=@psi-2 REFERENCE=1.25 LABEL=c2
c2_torsionsThe TORSION action with label c2_torsions calculates the following quantities:| Quantity | Type | Description |
| c2_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the 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.
c2_refThe CONSTANT action with label c2_ref calculates the following quantities:| Quantity | Type | Description |
| c2_ref | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.25
c2_coeffThe CONSTANT action with label c2_coeff calculates the following quantities:| Quantity | Type | Description |
| c2_coeff | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1
c2_combThe COMBINE action with label c2_comb calculates the following quantities:| Quantity | Type | Description |
| c2_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c2_torsions,c2_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c2_cosThe CUSTOM action with label c2_cos calculates the following quantities:| Quantity | Type | Description |
| c2_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c2_comb,c2_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c2The SUM action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c2_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c4The ALPHABETA action with label c4 calculates the following quantities:| Quantity | Type | Description |
| c4 | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=@psi-3 REFERENCE=1.25 LABEL=c4
c4_torsionsThe TORSION action with label c4_torsions calculates the following quantities:| Quantity | Type | Description |
| c4_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.
c4_refThe CONSTANT action with label c4_ref calculates the following quantities:| Quantity | Type | Description |
| c4_ref | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.25
c4_coeffThe CONSTANT action with label c4_coeff calculates the following quantities:| Quantity | Type | Description |
| c4_coeff | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1
c4_combThe COMBINE action with label c4_comb calculates the following quantities:| Quantity | Type | Description |
| c4_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c4_torsions,c4_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c4_cosThe CUSTOM action with label c4_cos calculates the following quantities:| Quantity | Type | Description |
| c4_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c4_comb,c4_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c4The SUM action with label c4 calculates the following quantities:| Quantity | Type | Description |
| c4 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c4_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. This action is a shortcut. More details ATOMS1the atoms involved for each of the torsions you wish to calculate=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. REFERENCEthe reference values for each of the torsional angles=1.25 LABELa label for the action so that its output can be referenced in the input to other actions=c6The ALPHABETA action with label c6 calculates the following quantities:| Quantity | Type | Description |
| c6 | scalar | the alpha beta CV |
# ALPHABETA ATOMS1=@psi-4 REFERENCE=1.25 LABEL=c6
c6_torsionsThe TORSION action with label c6_torsions calculates the following quantities:| Quantity | Type | Description |
| c6_torsions | vector | the TORSION for each set of specified atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMS1the four atoms involved in the torsional angle=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.
c6_refThe CONSTANT action with label c6_ref calculates the following quantities:| Quantity | Type | Description |
| c6_ref | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.25
c6_coeffThe CONSTANT action with label c6_coeff calculates the following quantities:| Quantity | Type | Description |
| c6_coeff | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1
c6_combThe COMBINE action with label c6_comb calculates the following quantities:| Quantity | Type | Description |
| c6_comb | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c6_torsions,c6_ref COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c6_cosThe CUSTOM action with label c6_cos calculates the following quantities:| Quantity | Type | Description |
| c6_cos | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c6_comb,c6_coeff FUNCthe function you wish to evaluate=y*(0.5+0.5*cos(x)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c6The SUM action with label c6 calculates the following quantities:| Quantity | Type | Description |
| c6 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=c6_cos PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=sum_absThe COMBINE action with label sum_abs calculates the following quantities:| Quantity | Type | Description |
| sum_abs | scalar | a linear compbination |
ARGthe values input to this function=c1,c2,c3,c4,c5,c6 POWERS the powers to which you are raising each of the arguments in your function=1,1,1,1,1,1 COEFFICIENTS the coefficients of the arguments in your function=0.6228,0.1201,0.5643,0.1102,0.5153,0.0403 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=sum_abs
HEIGHTthe heights of the Gaussian hills=0.4
BIASFACTORuse well tempered metadynamics and use this bias factor=4
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
SIGMAthe widths of the Gaussian hills=0.04
GRID_MINthe lower bounds for the grid=-0.02 GRID_MAXthe upper bounds for the grid=2.0 GRID_BINthe number of bins for the grid=200
LABELa label for the action so that its output can be referenced in the input to other actions=WTMetaDThe METAD action with label WTMetaD calculates the following quantities:| Quantity | Type | Description |
| WTMetaD.bias | scalar | the instantaneous value of the bias potential |
| WTMetaD.acc | scalar | the metadynamics acceleration factor |
| WTMetaD.pace | scalar | the hill addition frequency when employing frequency adaptive metadynamics |
FREQUENCY_ADAPTIVE Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor
PACEthe frequency for hill addition=1000
FA_MAX_PACEthe maximum hill addition frequency allowed in frequency adaptive metadynamics=100000
FA_UPDATE_FREQUENCYthe frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE=500
FA_MIN_ACCELERATIONonly update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here=1e1
ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=sum_abs
HEIGHTthe heights of the Gaussian hills=0.4
BIASFACTORuse well tempered metadynamics and use this bias factor=4
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
SIGMAthe widths of the Gaussian hills=0.04
GRID_MINthe lower bounds for the grid=-0.02 GRID_MAXthe upper bounds for the grid=2.0 GRID_BINthe number of bins for the grid=200
LABELa label for the action so that its output can be referenced in the input to other actions=WTMetaD
FREQUENCY_ADAPTIVE Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor
PACEthe frequency for hill addition=1000
FA_MAX_PACEthe maximum hill addition frequency allowed in frequency adaptive metadynamics=100000
FA_UPDATE_FREQUENCYthe frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE=500
FA_MIN_ACCELERATIONonly update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here=1e1
ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor
FILE a file in which the list of added hills is stored=HILLS
... METAD
COMMITTORDoes a committor analysis. More details ...
ARGthe labels of the values which is being used to define the committor surface=sum_abs
STRIDE the frequency with which the CVs are analyzed=5000
BASIN_LL1List of lower limits for basin #=1.85
BASIN_UL1List of upper limits for basin #=2.0
... COMMITTOR
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=sum_abs,WTMetaD.* FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%12.5f
