PLUMED-NEST

Project ID: plumID:20.007
Source: double/plumed.dat
Originally used with PLUMED version: 2.4.2
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

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-2640

d686_1739The DISTANCE action with label d686_1739 calculates the following quantities:
 Quantity   
 Type   
 Description  
d686_1739
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=686,1739
d1834_1853The DISTANCE action with label d1834_1853 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1834_1853
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1834,1853
d1732_1739The DISTANCE action with label d1732_1739 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1732_1739
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1732,1739
d1755_1765The DISTANCE action with label d1755_1765 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1755_1765
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1755,1765
d1823_1834The DISTANCE action with label d1823_1834 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1823_1834
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1823,1834
d1765_1823The DISTANCE action with label d1765_1823 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1765_1823
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1765,1823
d1809_1877The DISTANCE action with label d1809_1877 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1809_1877
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1809,1877
d1187_1739The DISTANCE action with label d1187_1739 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1187_1739
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1187,1739
d1877_1894The DISTANCE action with label d1877_1894 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1877_1894
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1877,1894
d1853_1947The DISTANCE action with label d1853_1947 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1853_1947
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1853,1947

psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1773,1775,1791,1793
distThe DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1772,1822 # A1130-S117H

rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=rmsd.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=rmsd.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc1The COMBINE action with label rc1 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc1
scalar
a linear compbination 
ARGthe values input to this function=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947 
COEFFICIENTS the coefficients of the arguments in your function=0.135,-0.343,0.432,0.348,-0.377,0.162,-0.138,0.294,0.527,-0.070
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc2The COMBINE action with label rc2 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc2
scalar
a linear compbination 
ARGthe values input to this function=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947 
COEFFICIENTS the coefficients of the arguments in your function=-0.075,-0.226,0.758,0.083,-0.326,0.247,-0.173,-0.137,0.194,0.330
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE


METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
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
ARGthe labels of the scalars on which the bias will act=rc1,rc2
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=1.5
SIGMAthe widths of the Gaussian hills=0.021,0.014
BIASFACTORuse well tempered metadynamics and use this bias factor=10.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metad
ARGthe labels of the scalars on which the bias will act=rc1,rc2
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=1.5
SIGMAthe widths of the Gaussian hills=0.021,0.014
BIASFACTORuse well tempered metadynamics and use this bias factor=10.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
 FILE a file in which the list of added hills is stored=HILLS
... METAD

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=.4 KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=4 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.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=d686_1739,d1834_1853,d1732_1739,d1755_1765,d1823_1834,d1765_1823,d1809_1877,d1187_1739,d1877_1894,d1853_1947,rc1,rc2,psi,dist,rmsd,uwall.bias,metad.bias STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR_full