Project ID: plumID:24.008
Source: Uracil/Volume_MetaD_Input/plumed_run.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 detailsSTRUCTURE=../Structure/yCD_uracil.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 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=4859-4870the 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
# 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_UR2the 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=sphreference atoms
# Now we need to remake whole moleculesWHOLEMOLECULESThis 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=4859-4870the atoms that make up a molecule that you wish to alignENTITY4=4957-4959the atoms that make up a molecule that you wish to alignENTITY5=4960-4962the 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/chainA_template.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performed
# Fix fix:FIXEDATOMAdd 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
# Define volume based CVs 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
# Restraining potential of the sphere restr:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rhothe arguments on which the bias is actingAT=2.8the positions of the wallKAPPA=200 restr2:the force constant for the wallUPPER_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
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=rho,theta,phithe input for this action is the scalar output from one or more other actionsGRID_MIN=0,0.,-pithe lower bounds for the gridGRID_MAX=5,pi,pithe upper bounds for the gridSIGMA=0.1,pi/16.,pi/8the widths of the Gaussian hillsHEIGHT=1.2the heights of the Gaussian hillsPACE=500the frequency for hill additionBIASFACTOR=20use 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 quantities to a file. More detailsARG=rho,disthe input for this action is the scalar output from one or more other actionsFILE=distance.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=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 outputPrint quantities to a file. More detailsARG=restrthe input for this action is the scalar output from one or more other actionsFILE=sphere_restraint.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=abs.x,abs.y,abs.z,rel_x,rel_y,rel_zthe input for this action is the scalar output from one or more other actionsFILE=xyz_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=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=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 flushed