Project ID: plumID:21.021
Source: meta_inputs/tetrapept_2D/plumed_biased.dat
Originally used with PLUMED version: 2.7-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths
t1:TORSIONCalculate a torsional angle. More detailsATOMS=5,7,9,15 t2:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=7,9,15,17 t3:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=15,17,19,25 t4:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=17,19,25,27 t5:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=25,27,29,35 t6:the four atoms involved in the torsional angleTORSIONCalculate a torsional angle. More detailsATOMS=27,29,35,37the four atoms involved in the torsional angleWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-42 gyr:the atoms that make up a molecule that you wish to alignGYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=5,15,25,35,9,19,29,11,21,31,2,39,7,17,27,37,6,16,26,36the group of atoms that you are calculating the Gyration Tensor for
hy:GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=8,18,28,38 ox:the numerical indexes for the set of atoms in the groupGROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More detailsATOMS=6,16,26,36 c1:the numerical indexes for the set of atoms in the groupCOORDINATIONCalculate coordination numbers. More detailsGROUPA=oxFirst list of atomsGROUPB=hySecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={CUBIC D_0=3 D_MAX=4}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveMETAD...Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More detailsPACE=500the frequency for hill additionARG=gyr,c1the input for this action is the scalar output from one or more other actionsGRID_MIN=2.0,0.2the lower bounds for the gridGRID_MAX=5,15the upper bounds for the gridGRID_BIN=600,600the number of bins for the gridSIGMA=0.05,0.1the widths of the Gaussian hillsBIASFACTOR=5use well tempered metadynamics and use this bias factorHEIGHT=0.05the heights of the Gaussian hillsTEMP=300 ... mt:the system temperature - this is only needed if you are doing well-tempered metadynamicsPrint quantities to a file. More detailsARG=t1,t2,t3,t4,t5,t6the input for this action is the scalar output from one or more other actionsFILE=dihedralthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=mt.biasthe input for this action is the scalar output from one or more other actionsFILE=mt.gbiasthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=gyr,c1the input for this action is the scalar output from one or more other actionsFILE=colvarthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be output