Project ID: plumID:23.011
Source: Alanine/OneOPES_MultiCV/2/plumed.dat
Originally used with PLUMED version: 2.9
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.
omegaThe TORSION action with label omega calculates the following quantities:| Quantity | Type | Description |
| omega | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@omega-2the four atoms that are required to calculate the omega 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=2,19
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=6,17
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=7,16
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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_EXPLORE 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=psi
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2
FILE a file in which the list of all deposited kernels is stored=Kernels.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
PACEthe frequency for kernel deposition=5000
BARRIERthe free energy barrier to be overcome=50
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=psi
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2
FILE a file in which the list of all deposited kernels is stored=Kernels.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
PACEthe frequency for kernel deposition=5000
BARRIERthe free energy barrier to be overcome=50
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=opes1The OPES_METAD_EXPLORE action with label opes1 calculates the following quantities:| Quantity | Type | Description |
| opes1.bias | scalar | the instantaneous value of the bias potential |
| opes1.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes1.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes1.neff | scalar | effective sample size |
| opes1.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=d1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.02
FILE a file in which the list of all deposited kernels is stored=Kernels1.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
PACEthe frequency for kernel deposition=10000
BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=opes1
ARGthe labels of the scalars on which the bias will act=d1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.02
FILE a file in which the list of all deposited kernels is stored=Kernels1.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
PACEthe frequency for kernel deposition=10000
BARRIERthe free energy barrier to be overcome=3
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=opes2The OPES_METAD_EXPLORE action with label opes2 calculates the following quantities:| Quantity | Type | Description |
| opes2.bias | scalar | the instantaneous value of the bias potential |
| opes2.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes2.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes2.neff | scalar | effective sample size |
| opes2.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=d2
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.015
FILE a file in which the list of all deposited kernels is stored=Kernels2.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed2.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed2.Kernels
PACEthe frequency for kernel deposition=10000
BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=opes2
ARGthe labels of the scalars on which the bias will act=d2
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.015
FILE a file in which the list of all deposited kernels is stored=Kernels2.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed2.Kernels
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed2.Kernels
PACEthe frequency for kernel deposition=10000
BARRIERthe free energy barrier to be overcome=3
TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 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=opes.bias,phi,psi,ene,omega,d1,d2,d3,opes1.bias,opes2.bias FMTthe format that should be used to output real numbers=%7.4f
ENDPLUMEDTerminate plumed input. More details
