Project ID: plumID:23.016
Source: plumed.dat
Originally used with PLUMED version: 2.5.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#RESTART MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=adr_bin_ref.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-4903 d1 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=489,4651 d2 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=887,1501 d3 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1570,2021 d4 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3257,3710 d5 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4112,4322 MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=Aindex ARGthe values input to this function=d1,d2,d3,d4,d5 VARthe names to give each of the arguments in the function=x,y,z,a,b FUNCthe function you wish to evaluate=((-14.43*x-7.62*y+9.11*z-6.32*a-5.22*b)+27.888) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
tm3-tm6_1 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1687,3710 tm3-tm6_2 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1687,3646 yy : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3133,4629 NPxxY_iRMSDCalculate 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=NPxxY_inact_backbone_adr.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL : PIF_iRMSDCalculate 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=PIF_inact_adr.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL : tm5 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2926,4461 meta : METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=Aindex SIGMAthe widths of the Gaussian hills=0.1 HEIGHTthe heights of the Gaussian hills=1 PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=../HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=5. GRID_MINthe lower bounds for the grid=-50 GRID_MAXthe upper bounds for the grid=50 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR 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