Project ID: plumID:24.008
Source: Uracil/iMetaD/plumed_imetad.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# Reference structureMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=../Structure/yCD_uracil.pdb # Keep molecules wholea file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-2423the atoms that make up a molecule that you wish to alignENTITY1=2424-4846the atoms that make up a molecule that you wish to alignENTITY2=4847-4858the atoms that make up a molecule that you wish to alignENTITY3=4859-4870 # Fit heavy atoms to templatethe atoms that make up a molecule that you wish to alignFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsREFERENCE=../Structure/heavy_atoms.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performed
# Contactmap of atoms for path CV f1:CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More detailsATOMS1=4850,895the atoms involved in each of the contacts you wish to calculateATOMS2=4850,917the atoms involved in each of the contacts you wish to calculateATOMS3=4850,1671the atoms involved in each of the contacts you wish to calculateATOMS4=4850,2314the atoms involved in each of the contacts you wish to calculateATOMS5=4850,2423the atoms involved in each of the contacts you wish to calculateSWITCH={RATIONAL R_0=1.2}The switching functions to use for each of the contacts in your map
path2:PATHPath collective variables with a more flexible framework for the distance metric being used. More detailsREFERENCE=outpath.pdba pdb file containing the set of reference configurationsTYPE=EUCLIDEANthe manner in which distances are calculatedGPATHcalculate the trigonometric pathNOSPATHdo not calculate the spath CVNOZPATHdo not calculate the zpath CV
# Group definitions sph: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 detailsNDX_FILE=../Structure/index.ndxthe name of index file (gromacs syntax)NDX_GROUP=ChainA-H_ZN-ChainA url:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=../Structure/index.ndxthe name of index file (gromacs syntax)NDX_GROUP=UR1_noH lig:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=../Structure/index.ndxthe name of index file (gromacs syntax)NDX_GROUP=UR1 ref:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=../Structure/index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Protein-H_ZN # Group sys sys:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=../Structure/index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Protein_ZN_UR1_UR2 # This is the new water group definitionthe name of the group to be imported (gromacs syntax) - first group found is used by defaultWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More detailsATOMS=ligwrapped atomsAROUND=sph # Fixed atom fix:reference atomsFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=-1.101616,-0.678271,0.017793coordinates of the virtual atom
sph_center:COMCalculate the center of mass for a group of atoms. More detailsATOMS=sph url_center:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=urlthe list of atoms which are involved the virtual atom's definition
dis:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=sph_center,fixthe pair of atom that we are calculating the distance between
# We are not going to be biasing these coordinates but we can print them for reference abs:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=url_center,sph_centerthe pair of atom that we are calculating the distance betweenCOMPONENTSrho:calculate the x, y and z components of the distance separately and store them as labelDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=url_center,sph_center rel_x:the pair of atom that we are calculating the distance betweenMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs.z,abs.ythe input to this functionFUNC=(x-y)/sqrt(2the function you wish to evaluatePERIODIC=NO rel_y:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs.xthe input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO rel_z:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs.z,abs.ythe input to this functionFUNC=(x+y)/sqrt(2the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
theta:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=rel_z,rhothe input to this functionFUNC=acos(x/ythe function you wish to evaluatePERIODIC=0.,pi phi:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=rel_x,rel_ythe input to this functionFUNC=atan2(y,xthe function you wish to evaluatePERIODIC=-pi,piif the output of your function is periodic then you should specify the periodicity of the function
rmsd:RMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=../Structure/heavy_atoms_UR2.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performed
# Keep the restraint on the rmsd restr2:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rmsdthe arguments on which the bias is actingAT=0.1the positions of the wallKAPPA=200the force constant for the wall
# Coordination number c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=urlFirst list of atomsGROUPB=sphSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.45The r_0 parameter of the switching function
# For the second CV we need the atoms in the pocketINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=groups.dat pocket_center:file to be includedCOMCalculate the center of mass for a group of atoms. More detailsATOMS=pocketthe list of atoms which are involved the virtual atom's definition
d2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=url_center,pocket_centerthe pair of atom that we are calculating the distance between
## This is a CV for monitoring the unbinding progress cc:COORDINATIONCalculate coordination numbers. More detailsGROUPA=4847,4855,4852First list of atomsGROUPB=926,927,725,2378,2377,2423Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=1.0The r_0 parameter of the switching function
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=path2.gspath,d2 # bias the new CVsthe input for this action is the scalar output from one or more other actionsGRID_MIN=0,0the lower bounds for the gridGRID_MAX=10,10the upper bounds for the gridSIGMA=0.13,0.02 # sigma taken from reference (Karen Palacio-Rodriguez et. al)the widths of the Gaussian hillsHEIGHT=1.5the heights of the Gaussian hillsPACE=50000 # change to a large number for infrequent metadynamicsthe frequency for hill additionBIASFACTOR=15use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=metada label for the action so that its output can be referenced in the input to other actionsCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# print everythingPrint quantities to a file. More detailsARG=cc,path2.gspath,path2.gzpath,d2,metadthe input for this action is the scalar output from one or more other actionsFILE=metad_data.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be output
# for referencePrint quantities to a file. More detailsARG=rho,theta,phithe input for this action is the scalar output from one or more other actionsFILE=rtp_coord.datthe 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=cthe input for this action is the scalar output from one or more other actionsFILE=all_coordination_45.datthe 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=rmsd,restr2the input for this action is the scalar output from one or more other actionsFILE=rmsd_restraint.datthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputFLUSHThis 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 flushedCOMMITTOR...Does a committor analysis. More detailsARG=ccthe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the CVs are analyzedBASIN_LL1=-0.01List of lower limits for basin #BASIN_UL1=0.01 ...List of upper limits for basin #