Project ID: plumID:21.029
Source: ala3/parallel/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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=ala3.pdb
The MOLINFO 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=500
energyThe ENERGY action with label energy calculates the following quantities:| Quantity | Type | Description |
| energy | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
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=5,7,9,15 NOPBC ignore the periodic boundary conditions when calculating distances
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=7,9,15,17 NOPBC ignore the periodic boundary conditions when calculating distances
phi2The TORSION action with label phi2 calculates the following quantities:| Quantity | Type | Description |
| phi2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25 NOPBC ignore the periodic boundary conditions when calculating distances
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=17,19,25,27 NOPBC ignore the periodic boundary conditions when calculating distances
phi3The TORSION action with label phi3 calculates the following quantities:| Quantity | Type | Description |
| phi3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35 NOPBC ignore the periodic boundary conditions when calculating distances
psi3The TORSION action with label psi3 calculates the following quantities:| Quantity | Type | Description |
| psi3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37 NOPBC ignore the periodic boundary conditions when calculating distances
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=phi2 FILEthe name of the file containing the external potential=factor1.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor1The EXTERNAL action with label factor1 calculates the following quantities:| Quantity | Type | Description |
| factor1.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=phi2 FILEthe name of the file containing the external potential=factor1.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor1 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=phi1 FILEthe name of the file containing the external potential=factor2.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor2The EXTERNAL action with label factor2 calculates the following quantities:| Quantity | Type | Description |
| factor2.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=phi1 FILEthe name of the file containing the external potential=factor2.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor2 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=phi3 FILEthe name of the file containing the external potential=factor3.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor3The EXTERNAL action with label factor3 calculates the following quantities:| Quantity | Type | Description |
| factor3.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=phi3 FILEthe name of the file containing the external potential=factor3.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor3 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=psi2 FILEthe name of the file containing the external potential=factor4.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor4The EXTERNAL action with label factor4 calculates the following quantities:| Quantity | Type | Description |
| factor4.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=psi2 FILEthe name of the file containing the external potential=factor4.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor4 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=psi3 FILEthe name of the file containing the external potential=factor5.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor5The EXTERNAL action with label factor5 calculates the following quantities:| Quantity | Type | Description |
| factor5.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=psi3 FILEthe name of the file containing the external potential=factor5.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor5 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=psi1 FILEthe name of the file containing the external potential=factor6.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor6The EXTERNAL action with label factor6 calculates the following quantities:| Quantity | Type | Description |
| factor6.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=psi1 FILEthe name of the file containing the external potential=factor6.grid LABELa label for the action so that its output can be referenced in the input to other actions=factor6 SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
PRINTPrint quantities to a file. More details ...
ARGthe labels of the values that you would like to print to the file=phi1,psi1,phi2,psi2,phi3,psi3,factor1.bias,factor2.bias,factor3.bias,factor4.bias,factor5.bias,factor6.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
... PRINT
