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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsMOLTYPE=proteinwhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatibleSTRUCTURE=ala3.pdba file in pdb format containing a reference structureFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=500the frequency with which all the open files should be flushed
energy :ENERGYphi1 :Calculate the total potential energy of the simulation box. More detailsTORSIONCalculate a torsional angle. More detailsATOMS=5,7,9,15the four atoms involved in the torsional angleNOPBCpsi1 :ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=7,9,15,17the four atoms involved in the torsional angleNOPBCphi2 :ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=15,17,19,25the four atoms involved in the torsional angleNOPBCpsi2 :ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=17,19,25,27the four atoms involved in the torsional angleNOPBCphi3 :ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=25,27,29,35the four atoms involved in the torsional angleNOPBCpsi3 :ignore the periodic boundary conditions when calculating distancesTORSIONCalculate a torsional angle. More detailsATOMS=27,29,35,37the four atoms involved in the torsional angleNOPBCignore the periodic boundary conditions when calculating distancesEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More detailsARG=phi2the input for this action is the scalar output from one or more other actionsFILE=factor1.gridthe name of the file containing the external potentialLABEL=factor1a label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More detailsARG=phi1the input for this action is the scalar output from one or more other actionsFILE=factor2.gridthe name of the file containing the external potentialLABEL=factor2a label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More detailsARG=phi3the input for this action is the scalar output from one or more other actionsFILE=factor3.gridthe name of the file containing the external potentialLABEL=factor3a label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More detailsARG=psi2the input for this action is the scalar output from one or more other actionsFILE=factor4.gridthe name of the file containing the external potentialLABEL=factor4a label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More detailsARG=psi3the input for this action is the scalar output from one or more other actionsFILE=factor5.gridthe name of the file containing the external potentialLABEL=factor5a label for the action so that its output can be referenced in the input to other actionsEXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More detailsARG=psi1the input for this action is the scalar output from one or more other actionsFILE=factor6.gridthe name of the file containing the external potentialLABEL=factor6a label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARG=phi1,psi1,phi2,psi2,phi3,psi3,factor1.bias,factor2.bias,factor3.bias,factor4.bias,factor5.bias,factor6.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=1the frequency with which the quantities of interest should be outputFILE=COLVAR ... PRINTthe name of the file on which to output these quantities