PLUMED-NEST by 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
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=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={RATIONAL R_0=0.18 NN=6 MM=12} 
O1C: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
O1N: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
O1H: 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={RATIONAL R_0=0.15 NN=6 MM=12} 

C2O: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
C2C: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
C2N: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
C2H: 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={RATIONAL R_0=0.15 NN=6 MM=12} 

N3O: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
N3C: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
N3N: 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={RATIONAL R_0=0.18 NN=6 MM=12} 
N3H: 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={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)

pp: 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

uwall: 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:

metad: METADUsed to performed metadynamics on one or more collective variables. More details
 ARGthe input for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
Quantity	Description
metad.bias	the instantaneous value of the bias potential
PLUMED-NEST

The public repository of the PLUMED consortium
