PLUMED-NEST

Project ID: plumID:22.032
Source: 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

PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=path.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=1498 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 FULLSAMPLES number of samples in a bin prior to application of the ABF=2000 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=1 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=49 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1 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 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=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=200000 HISTORYFREQsave history to a file every N steps=2000000 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
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 FULLSAMPLES number of samples in a bin prior to application of the ABF=2000 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=1 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=49 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1 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 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=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=200000 HISTORYFREQsave history to a file every N steps=2000000 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 MAXFACTOR maximum scaling factor of biasing force=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 SIGMAthe widths of the Gaussian hills=0.5 HEIGHTthe heights of the Gaussian hills=1.8 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=50 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1 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=(0.27-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=uwz_argThe CUSTOM action with label uwz_arg calculates the following quantities:
 Quantity   
 Type   
 Description  
uwz_arg
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=uwz_arg LABELa label for the action so that its output can be referenced in the input to other actions=uw_path_zThe BIASVALUE action with label uw_path_z calculates the following quantities:
 Quantity   
 Type   
 Description  
uw_path_z.bias
scalar
the instantaneous value of the bias potential
uw_path_z.uwz_arg_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 uwz_arg
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=path.sss FUNCthe function you wish to evaluate=(49-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=uws_argThe CUSTOM action with label uws_arg calculates the following quantities:
 Quantity   
 Type   
 Description  
uws_arg
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=uws_arg LABELa label for the action so that its output can be referenced in the input to other actions=uw_sssThe BIASVALUE action with label uw_sss calculates the following quantities:
 Quantity   
 Type   
 Description  
uw_sss.bias
scalar
the instantaneous value of the bias potential
uw_sss.uws_arg_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 uws_arg
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=path.sss FUNCthe function you wish to evaluate=(x-1)^-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=lws_argThe CUSTOM action with label lws_arg calculates the following quantities:
 Quantity   
 Type   
 Description  
lws_arg
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=lws_arg LABELa label for the action so that its output can be referenced in the input to other actions=lw_sssThe BIASVALUE action with label lw_sss calculates the following quantities:
 Quantity   
 Type   
 Description  
lw_sss.bias
scalar
the instantaneous value of the bias potential
lw_sss.lws_arg_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 lws_arg
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.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