Project ID: plumID:23.005
Source: apo-5HT1A/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
#RESTARTMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=5ht1a_rec_ref.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsSTRIDE=1the frequency with which molecules are reassembledENTITY0=1-4932the atoms that make up a molecule that you wish to align
d1 :DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=394,4660 d2 :the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=770,1383 d3 :the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1457,1916 d4 :the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3028,3740 d5 :the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=4140,4352the pair of atom that we are calculating the distance betweenMATHEVAL...An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsLABEL=Aindexa label for the action so that its output can be referenced in the input to other actionsARG=d1,d2,d3,d4,d5the values input to this functionVAR=x,y,z,a,bthe names to give each of the arguments in the functionFUNC=((-14.43*x-7.62*y+9.11*z-6.32*a-5.22*b)+27.888the function you wish to evaluatePERIODIC=NO ... MATHEVALif the output of your function is periodic then you should specify the periodicity of the function
tm3-tm6_1 :DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3740,1574 tm3-tm6_2 :the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3665,1574 NPxxYthe pair of atom that we are calculating the distance betweenRMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=NPxxY_act_backbone_5ht1a.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL : yy :the manner in which RMSD alignment is performedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2903,4639 PIF_athe pair of atom that we are calculating the distance betweenRMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=PIF_act_5ht1a.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL : tm5 :the manner in which RMSD alignment is performedDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2688,4468the pair of atom that we are calculating the distance between
meta :METADUsed to performed metadynamics on one or more collective variables. More detailsARG=Aindexthe labels of the scalars on which the bias will actSIGMA=0.1the widths of the Gaussian hillsHEIGHT=1the heights of the Gaussian hillsPACE=500the frequency for hill additionFILE=../HILLSa file in which the list of added hills is storedBIASFACTOR=5use well tempered metadynamics and use this bias factorGRID_MIN=-50the lower bounds for the gridGRID_MAX=50the upper bounds for the gridCALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]TEMP=310the system temperature - this is only needed if you are doing well-tempered metadynamicsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRPrint quantities to a file. More detailsARGthe labels of the values that you would like to print to the fileSTRIDE=500the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities