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
Click on the labels of the actions for more information on what each action computes
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# Reference structure 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=../Structure/yCD_uracil.pdb # Keep molecules whole WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-2423 ENTITY1the atoms that make up a molecule that you wish to align=2424-4846 ENTITY2the atoms that make up a molecule that you wish to align=4847-4858 ENTITY3the atoms that make up a molecule that you wish to align=4859-4870 # Fit heavy atoms to template FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../Structure/heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL # 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 details ATOMS1the atoms involved in each of the contacts you wish to calculate=4850,895 ATOMS2the atoms involved in each of the contacts you wish to calculate=4850,917 ATOMS3the atoms involved in each of the contacts you wish to calculate=4850,1671 ATOMS4the atoms involved in each of the contacts you wish to calculate=4850,2314 ATOMS5the atoms involved in each of the contacts you wish to calculate=4850,2423 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.2}
path2: PATHPath collective variables with a more flexible framework for the distance metric being used. This action is a shortcut. More details REFERENCEa pdb file containing the set of reference configurations=outpath.pdb TYPE the manner in which distances are calculated=EUCLIDEAN GPATH calculate the trigonometric path NOSPATH do not calculate the spath CV NOZPATH do 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 details NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=ChainA-H_ZN-ChainA url: 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 details NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=UR1_noH lig: 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 details NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=UR1 ref: 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 details NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H_ZN # Group sys sys: 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 details NDX_FILEthe name of index file (gromacs syntax)=../Structure/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein_ZN_UR1_UR2 # This is the new water group definition
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=lig AROUNDreference atoms=sph # Fixed atom fix: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=-1.101616,-0.678271,0.017793
sph_center: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=sph url_center: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=url dis: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=sph_center,fix # We are not going to be biasing these coordinates but we can print them for reference abs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=url_center,sph_center COMPONENTS calculate the x, y and z components of the distance separately and store them as label rho: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=url_center,sph_center rel_x: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs.z,abs.y FUNCthe function you wish to evaluate=(x-y)/sqrt(2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rel_y: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs.x FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rel_z: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs.z,abs.y FUNCthe function you wish to evaluate=(x+y)/sqrt(2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO theta: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=rel_z,rho FUNCthe function you wish to evaluate=acos(x/y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=0.,pi phi: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=rel_x,rel_y FUNCthe function you wish to evaluate=atan2(y,x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-pi,pi rmsd: RMSDCalculate 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=../Structure/heavy_atoms_UR2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
# Keep the restraint on the rmsd restr2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.1 KAPPAthe force constant for the wall=200 # Coordination number c: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=url GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=sph R_0The r_0 parameter of the switching function=0.45
# For the second CV we need the atoms in the pocket INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=groups.dat pocket_center: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=pocket d2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=url_center,pocket_center ## This is a CV for monitoring the unbinding progress cc: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=4847,4855,4852 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=926,927,725,2378,2377,2423 R_0The r_0 parameter of the switching function=1.0
# Metadynamics METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... ARGthe labels of the scalars on which the bias will act=path2.gspath,d2 # bias the new CVs GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=10,10 SIGMAthe widths of the Gaussian hills=0.13,0.02 # sigma taken from reference (Karen Palacio-Rodriguez et. al) HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=50000 # change to a large number for infrequent metadynamics BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300. LABELa label for the action so that its output can be referenced in the input to other actions=metad CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] ... METAD
# print everything PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cc,path2.gspath,path2.gzpath,d2,metad.* FILEthe name of the file on which to output these quantities=metad_data.dat STRIDE the frequency with which the quantities of interest should be output=500 # for reference PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho,theta,phi FILEthe name of the file on which to output these quantities=rtp_coord.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c FILEthe name of the file on which to output these quantities=all_coordination_45.dat STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd,restr2.* FILEthe name of the file on which to output these quantities=rmsd_restraint.dat STRIDE the frequency with which the quantities of interest should be output=500 FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=500 COMMITTORDoes a committor analysis. More details ... ARGthe labels of the values which is being used to define the committor surface=cc STRIDE the frequency with which the CVs are analyzed=5000 BASIN_LL1List of lower limits for basin #=-0.01 BASIN_UL1List of upper limits for basin #=0.01 ...