Project ID: plumID:23.007
Source: plumed-nest/nrpe3/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
WHOLEMOLECULESThis 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=1-73
The WHOLEMOLECULES action with label calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cn.dat
# INCLUDE FILE=cn.dat
The INCLUDE action with label cn.dat calculates somethingr1The COM action with label r1 calculates the following quantities:| Quantity | Type | Description |
| r1 | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=13,22
r2The COM action with label r2 calculates the following quantities:| Quantity | Type | Description |
| r2 | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=41,50
r3The COM action with label r3 calculates the following quantities:| Quantity | Type | Description |
| r3 | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=63,72
cThe COORDINATION action with label c calculates the following quantities:| Quantity | Type | Description |
| c | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1,r1,r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2,r3,r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
c1The COORDINATION action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
c2The COORDINATION action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
c3The COORDINATION action with label c3 calculates the following quantities:| Quantity | Type | Description |
| c3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
# --- End of included input --- INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cv.dat
# INCLUDE FILE=cv.dat
The INCLUDE action with label cv.dat calculates somethingphi0The TORSION action with label phi0 calculates the following quantities:| Quantity | Type | Description |
| phi0 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=24,4,3,1
phi1The TORSION action with label phi1 calculates the following quantities:| Quantity | Type | Description |
| phi1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,32,31,29
psi0The TORSION action with label psi0 calculates the following quantities:| Quantity | Type | Description |
| psi0 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=26,24,4,3
psi1The TORSION action with label psi1 calculates the following quantities:| Quantity | Type | Description |
| psi1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,1,32,31
psi2The TORSION action with label psi2 calculates the following quantities:| Quantity | Type | Description |
| psi2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,29,54,52
omega0The TORSION action with label omega0 calculates the following quantities:| Quantity | Type | Description |
| omega0 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,1,32
omega1The TORSION action with label omega1 calculates the following quantities:| Quantity | Type | Description |
| omega1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=32,31,29,54
chi0The TORSION action with label chi0 calculates the following quantities:| Quantity | Type | Description |
| chi0 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,7,13
chi1The TORSION action with label chi1 calculates the following quantities:| Quantity | Type | Description |
| chi1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=32,31,35,41
chi2The TORSION action with label chi2 calculates the following quantities:| Quantity | Type | Description |
| chi2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=54,52,57,63
chi20The TORSION action with label chi20 calculates the following quantities:| Quantity | Type | Description |
| chi20 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,7,13,9
chi21The TORSION action with label chi21 calculates the following quantities:| Quantity | Type | Description |
| chi21 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,35,41,37
chi22The TORSION action with label chi22 calculates the following quantities:| Quantity | Type | Description |
| chi22 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=52,57,63,58
# --- End of included input --- INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=imp.dat
# INCLUDE FILE=imp.dat
The INCLUDE action with label imp.dat calculates somethingimp0The TORSION action with label imp0 calculates the following quantities:| Quantity | Type | Description |
| imp0 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,8,9,13
imp1The TORSION action with label imp1 calculates the following quantities:| Quantity | Type | Description |
| imp1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=35,36,37,41
imp2The TORSION action with label imp2 calculates the following quantities:| Quantity | Type | Description |
| imp2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=57,58,59,63
# --- End of included input ---
rgThe GYRATION action with label rg calculates the following quantities:| Quantity | Type | Description |
| rg | scalar | the radius of gyration |
: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,3,4,29,31,32,52,54
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=imp0,imp1,imp2 ATthe position of the restraint=-0.7,-0.7,-0.7 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=150,150,150 LABELa label for the action so that its output can be referenced in the input to other actions=restraintThe RESTRAINT action with label restraint calculates the following quantities:| Quantity | Type | Description |
| restraint.bias | scalar | the instantaneous value of the bias potential |
| restraint.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=imp0,imp1,imp2 ATthe position of the restraint=-0.7,-0.7,-0.7 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=150,150,150 LABELa label for the action so that its output can be referenced in the input to other actions=restraint SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0,0.0,0.0
PBMETADUsed to performed Parallel Bias metadynamics. More details ...
ARGthe labels of the scalars on which the bias will act=c,c1,c2,c3,rg,omega0,omega1,phi0,phi1,psi0,psi1,psi2,chi0,chi1,chi2
SIGMAthe widths of the Gaussian hills=0.5,0.5,0.5,0.5,0.1,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35
HEIGHTthe height of the Gaussian hills, one for all biases=2.5
PACEthe frequency for hill addition, one for all biases=500
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=50
GRID_MINthe lower bounds for the grid=-1,-1,-1,-1,-1,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi
GRID_MAXthe upper bounds for the grid=20,20,20,20,20,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
LABELa label for the action so that its output can be referenced in the input to other actions=pbThe PBMETAD action with label pb calculates the following quantities:| Quantity | Type | Description |
| pb.bias | scalar | the instantaneous value of the bias potential |
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_c,HILLS_c1,HILLS_c2,HILLS_c3,HILLS_rg,HILLS_omega0,HILLS_omega1,HILLS_phi0,HILLS_phi1,HILLS_psi0,HILLS_psi1,HILLS_psi2,HILLS_chi0,HILLS_chi1,HILLS_chi2
... PBMETAD
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=500 FILEthe name of the file on which to output these quantities=COLVAR
