PLUMED-NEST

Project ID: plumID:23.013
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

#RESTART
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=nm TIMEthe units of time=ps ENERGYthe units of energy=kj/mol
The UNITS action with label  calculates somethingTIMEretrieve the time of the simulation to be used elsewhere More details LABELa label for the action so that its output can be referenced in the input to other actions=timThe TIME action with label tim calculates the following quantities:
 Quantity   
 Type   
 Description  
tim
scalar
the time since the start of the trajectory
PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=sting-traj-based-path-CA+MET-SD.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=1158 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)=32 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05 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=250000 HISTORYFREQsave history to a file every N steps=2500000 DRR_RFILEspecifies the restart file (=drr 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)=32 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05 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=250000 HISTORYFREQsave history to a file every N steps=2500000 DRR_RFILEspecifies the restart file (=drr 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=0.25 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=33 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05 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=tim FUNCthe function you wish to evaluate=0.5*(erf((200-x)*0.1)+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=stp1The CUSTOM action with label stp1 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp1
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((x-200)*0.1)+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=stp2The CUSTOM action with label stp2 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp2
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((300-x)*0.1)+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=stp3The CUSTOM action with label stp3 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp3
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((x-300)*0.1)+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=stp4The CUSTOM action with label stp4 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp4
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((400-x)*0.1)+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=stp5The CUSTOM action with label stp5 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp5
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((x-400)*0.1)+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=stp6The CUSTOM action with label stp6 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp6
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((500-x)*0.1)+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=stp7The CUSTOM action with label stp7 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp7
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=tim FUNCthe function you wish to evaluate=0.5*(erf((x-500)*0.1)+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=stp8The CUSTOM action with label stp8 calculates the following quantities:
 Quantity   
 Type   
 Description  
stp8
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=stp1,stp2,stp3,stp4,stp5,stp6,stp7,stp8 VARthe names to give each of the arguments in the function=x1,x2,x3,x4,x5,x6,x7,x8 FUNCthe function you wish to evaluate=0.15*x1+0.125*x2*x3+0.1*x4*x5+0.075*x6*x7+0.05*x8 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=max_zThe CUSTOM action with label max_z calculates the following quantities:
 Quantity   
 Type   
 Description  
max_z
scalar
an arbitrary function
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=path_z,max_z FUNCthe function you wish to evaluate=(y-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
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=32 KAPPAthe force constant for the wall=1000 LABELa label for the action so that its output can be referenced in the input to other actions=uw_sThe UPPER_WALLS action with label uw_s calculates the following quantities:
 Quantity   
 Type   
 Description  
uw_s.bias
scalar
the instantaneous value of the bias potential
uw_s.force2
scalar
the instantaneous value of the squared force due to this bias potential
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=1  KAPPAthe force constant for the wall=1000 LABELa label for the action so that its output can be referenced in the input to other actions=lw_sThe LOWER_WALLS action with label lw_s calculates the following quantities:
 Quantity   
 Type   
 Description  
lw_s.bias
scalar
the instantaneous value of the bias potential
lw_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=drr.path.sss_fict ATthe positions of the wall=32 KAPPAthe force constant for the wall=1000 LABELa label for the action so that its output can be referenced in the input to other actions=uw_s_fictThe UPPER_WALLS action with label uw_s_fict calculates the following quantities:
 Quantity   
 Type   
 Description  
uw_s_fict.bias
scalar
the instantaneous value of the bias potential
uw_s_fict.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=drr.path.sss_fict ATthe positions of the wall=1  KAPPAthe force constant for the wall=1000 LABELa label for the action so that its output can be referenced in the input to other actions=lw_s_fictThe LOWER_WALLS action with label lw_s_fict calculates the following quantities:
 Quantity   
 Type   
 Description  
lw_s_fict.bias
scalar
the instantaneous value of the bias potential
lw_s_fict.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-force.log FMTthe format that should be used to output real numbers=%12.4f
FLUSHThis 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