Project ID: plumID:23.012
Source: plumed.dat
Originally used with PLUMED version: 2.8.1
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
PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=path-CV-equidistant-mcnally.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=51250 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4 NEIGH_SIZEsize of the neighbor list=8 LABELa label for the action so that its output can be referenced in the input to other actions=pathThe PATHMSD action with label path calculates the following quantities:| Quantity | Type | Description |
| path.sss | scalar | the position on the path |
| path.zzz | scalar | the distance from the path |
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=path.zzz FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=path_zThe CUSTOM action with label path_z calculates the following quantities:| Quantity | Type | Description |
| path_z | scalar | an arbitrary function |
DRRUsed to performed extended-system adaptive biasing force(eABF) This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=path.sss,path_z KAPPAspecifies that the restraint is harmonic and what the values of the force constants on each of the variables are (default to k_BT/(GRID_SPACING)^2)=250,2.5e6 FULLSAMPLES number of samples in a bin prior to application of the ABF=500 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=2,0.0 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=27,0.045 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.001 TEMPthe system temperature - needed when FRICTION is present=310 FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=8.0,8.0 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=0.5,0.5 TEXTOUTPUT use text output for grad and count files instead of boost::serialization binary output OUTPUTFREQwrite results to a file every N steps=100000 HISTORYFREQsave history to a file every N steps=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=drrThe DRR action with label drr calculates the following quantities:| Quantity | Type | Description |
| drr.bias | scalar | the instantaneous value of the bias potential |
| drr.path.sss_fict | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is possible to add forces on these variable. This particular component measures this quantity for the input CV named path.sss |
| drr.path.sss_vfict | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is NOT possible to add forces on these variable. This particular component measures this quantity for the input CV named path.sss |
| drr.path.sss_biasforce | scalar | The bias force from eABF/DRR of the fictitious particle. This particular component measures this quantity for the input CV named path.sss |
| drr.path.sss_springforce | scalar | Spring force between real CVs and extended CVs This particular component measures this quantity for the input CV named path.sss |
| drr.path.sss_fictNoPBC | scalar | the positions of fictitious particles (without PBC). This particular component measures this quantity for the input CV named path.sss |
| drr.path_z_fict | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is possible to add forces on these variable. This particular component measures this quantity for the input CV named path_z |
| drr.path_z_vfict | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is NOT possible to add forces on these variable. This particular component measures this quantity for the input CV named path_z |
| drr.path_z_biasforce | scalar | The bias force from eABF/DRR of the fictitious particle. This particular component measures this quantity for the input CV named path_z |
| drr.path_z_springforce | scalar | Spring force between real CVs and extended CVs This particular component measures this quantity for the input CV named path_z |
| drr.path_z_fictNoPBC | scalar | the positions of fictitious particles (without PBC). This particular component measures this quantity for the input CV named path_z |
DRRUsed to performed extended-system adaptive biasing force(eABF) This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=path.sss,path_z KAPPAspecifies that the restraint is harmonic and what the values of the force constants on each of the variables are (default to k_BT/(GRID_SPACING)^2)=250,2.5e6 FULLSAMPLES number of samples in a bin prior to application of the ABF=500 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=2,0.0 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=27,0.045 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.001 TEMPthe system temperature - needed when FRICTION is present=310 FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=8.0,8.0 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=0.5,0.5 TEXTOUTPUT use text output for grad and count files instead of boost::serialization binary output OUTPUTFREQwrite results to a file every N steps=100000 HISTORYFREQsave history to a file every N steps=1000000 LABELa label for the action so that its output can be referenced in the input to other actions=drr REFLECTINGWALL whether add reflecting walls for each CV at GRID_MIN and GRID_MAX=0,0 MAXFACTOR maximum scaling factor of biasing force=1.0,1.0
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=drr.path.sss_fict,drr.path_z_fict SIGMAthe widths of the Gaussian hills=0.5,0.005 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=0,-0.02 GRID_MAXthe upper bounds for the grid=29,0.06 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.001 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 FILE a file in which the list of added hills is stored=HILLS LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=path_z FUNCthe function you wish to evaluate=(0.05-x)^-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=custom_zThe CUSTOM action with label custom_z calculates the following quantities:| Quantity | Type | Description |
| custom_z | scalar | an arbitrary function |
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=custom_z LABELa label for the action so that its output can be referenced in the input to other actions=z_wallThe BIASVALUE action with label z_wall calculates the following quantities:| Quantity | Type | Description |
| z_wall.bias | scalar | the instantaneous value of the bias potential |
| z_wall.custom_z_bias | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named custom_z |
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=path.sss ATthe positions of the wall=3 OFFSET the offset for the start of the wall=0.0 KAPPAthe force constant for the wall=100 EPS the values for s_i in the expression for a wall=1.0 LABELa label for the action so that its output can be referenced in the input to other actions=lwall_sThe LOWER_WALLS action with label lwall_s calculates the following quantities:| Quantity | Type | Description |
| lwall_s.bias | scalar | the instantaneous value of the bias potential |
| lwall_s.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=path.sss ATthe positions of the wall=26 OFFSET the offset for the start of the wall=0.0 KAPPAthe force constant for the wall=100 EPS the values for s_i in the expression for a wall=1.0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_sThe UPPER_WALLS action with label uwall_s calculates the following quantities:| Quantity | Type | Description |
| uwall_s.bias | scalar | the instantaneous value of the bias potential |
| uwall_s.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=plumed-force2.log FMTthe format that should be used to output real numbers=%12.4f
The PRINT 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=1000
