PLUMED-NEST

Project ID: plumID:19.032
Source: plumed.dat
Originally used with PLUMED version: 2.4
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

#
# example of input: metadynamics simulation connecting formamide with CO+NH3
# units are nm and kJ/mol
#

RESTARTActivate restart. More details
The RESTART 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=10

# here below we set a coordination table with 3 rows (O1,C2,N3) and 4 columns (all O,C,N,H)

# the coordination functions are typically chosen so that covalent bond ~0.9, second neighbors < 0.2
# (note that X-X is longer than X-H, with X=O,C,N)

O1O: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1,7-68     LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label O1O calculates the following quantities:
 Quantity   
 Description  
O1O.lessthan
the number of colvars that have a value less than a threshold
O1O.value
the DISTANCES between the each pair of atoms that were specifiedO1C: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2          LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label O1C calculates the following quantities:
 Quantity   
 Description  
O1C.lessthan
the number of colvars that have a value less than a threshold
O1C.value
the DISTANCES between the each pair of atoms that were specifiedO1N: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3          LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label O1N calculates the following quantities:
 Quantity   
 Description  
O1N.lessthan
the number of colvars that have a value less than a threshold
O1N.value
the DISTANCES between the each pair of atoms that were specifiedO1H: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=4-6,69-192 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.15 NN=6 MM=12} 

The DISTANCES action with label O1H calculates the following quantities:
 Quantity   
 Description  
O1H.lessthan
the number of colvars that have a value less than a threshold
O1H.value
the DISTANCES between the each pair of atoms that were specifiedC2O: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1,7-68     LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label C2O calculates the following quantities:
 Quantity   
 Description  
C2O.lessthan
the number of colvars that have a value less than a threshold
C2O.value
the DISTANCES between the each pair of atoms that were specifiedC2C: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2          LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label C2C calculates the following quantities:
 Quantity   
 Description  
C2C.lessthan
the number of colvars that have a value less than a threshold
C2C.value
the DISTANCES between the each pair of atoms that were specifiedC2N: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3          LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label C2N calculates the following quantities:
 Quantity   
 Description  
C2N.lessthan
the number of colvars that have a value less than a threshold
C2N.value
the DISTANCES between the each pair of atoms that were specifiedC2H: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=4-6,69-192 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.15 NN=6 MM=12} 

The DISTANCES action with label C2H calculates the following quantities:
 Quantity   
 Description  
C2H.lessthan
the number of colvars that have a value less than a threshold
C2H.value
the DISTANCES between the each pair of atoms that were specifiedN3O: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1,7-68     LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label N3O calculates the following quantities:
 Quantity   
 Description  
N3O.lessthan
the number of colvars that have a value less than a threshold
N3O.value
the DISTANCES between the each pair of atoms that were specifiedN3C: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2          LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label N3C calculates the following quantities:
 Quantity   
 Description  
N3C.lessthan
the number of colvars that have a value less than a threshold
N3C.value
the DISTANCES between the each pair of atoms that were specifiedN3N: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3          LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.18 NN=6 MM=12} 
The DISTANCES action with label N3N calculates the following quantities:
 Quantity   
 Description  
N3N.lessthan
the number of colvars that have a value less than a threshold
N3N.value
the DISTANCES between the each pair of atoms that were specifiedN3H: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=4-6,69-192 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.15 NN=6 MM=12} 

# here below are defined path collective variables s,z based on coordination patterns:
# the switching function is (1-(dist/R_0)**NN)/(1-(dist/R_0)**MM) 
# LAMBDA is chosen so that the distance (sum of squares of coord. num. differences) between ref. structures is about 2.3
# the two ref. structures are specified in file path.pdb (more than 2 references can also be used)

The DISTANCES action with label N3H calculates the following quantities:
 Quantity   
 Description  
N3H.lessthan
the number of colvars that have a value less than a threshold
N3H.value
the DISTANCES between the each pair of atoms that were specifiedpp: PATHPath collective variables with a more flexible framework for the distance metric being used. More details REFERENCEa pdb file containing the set of reference configurations=path.pdb TYPE the manner in which distances are calculated=EUCLIDEAN LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=0.78  

# a wall may be used to limit to limit the largest z coordinates explored, as here below

The PATH action with label pp calculates the following quantities:
 Quantity   
 Description  
pp.spath
the position along the path calculated
pp.zpath
the distance from the path calculateduwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.zpath ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=2 

# metadynamics is performed on s,z:

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=pp.spath,pp.zpath SIGMAthe widths of the Gaussian hills=0.025,0.1 HEIGHTthe heights of the Gaussian hills=10 PACEthe frequency for hill addition=100 

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pp.spath,pp.zpath,metad.bias,uwall.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR