Project ID: plumID:21.018
Source: input/MacroD2_I189R_input/metad_35ang.dat
Originally used with PLUMED version: 2.6
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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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=1-3682 ENTITY1the atoms that make up a molecule that you wish to align=3683-3739 # Group definition prot_noh: 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)=ref_index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H 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)=ref_index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Prot_ref_noH AR6: 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)=ref_index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=AR6_noH ref_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=ref AR6_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=AR6 Fix: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=5.0,5.0,5.0 Dis: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ref_center,Fix ref_coord: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=ref_center NOPBC ignore the periodic boundary conditions when calculating distances AR6_coord: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=AR6_center NOPBC ignore the periodic boundary conditions when calculating distances
abs_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=AR6_coord.x,ref_coord.x FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO abs_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=AR6_coord.y,ref_coord.y FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO abs_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=AR6_coord.z,ref_coord.z FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 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_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_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_y,abs_z FUNCthe function you wish to evaluate=(x-sqrt(3)*y)/2 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_y,abs_z FUNCthe function you wish to evaluate=(sqrt(3)*x+y)/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rho: 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,abs_y,abs_z FUNCthe function you wish to evaluate=sqrt(x*x+y*y+z*z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO siga: 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=sqrt(-x+y) 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_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=ref_protein_noH_nosite.pdb TYPE the manner in which RMSD alignment is performed=SIMPLE
# Restraining potential of the sphere restr_dis: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=Dis ATthe positions of the wall=1.00 KAPPAthe force constant for the wall=20000 OFFSET the offset for the start of the wall=0 restr_rho: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rho ATthe positions of the wall=3.50 KAPPAthe force constant for the wall=20000 OFFSET the offset for the start of the wall=0 restr_siga: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=siga ATthe positions of the wall=1.0 KAPPAthe force constant for the wall=20000 OFFSET the offset for the start of the wall=0 restr_rmsd: 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=0.10 KAPPAthe force constant for the wall=20000 OFFSET the offset for the start of the wall=0 # Coordination number c: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=AR6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=prot_noh R_0The r_0 parameter of the switching function=0.45
# 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=rho,siga,theta GRID_MINthe lower bounds for the grid=0,0,-pi GRID_MAXthe upper bounds for the grid=3.6,1.2,pi SIGMAthe widths of the Gaussian hills=0.1,0.04,pi/8 HEIGHTthe heights of the Gaussian hills=1.2 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=restr_dis.*,restr_rho.*,restr_siga.*,restr_rmsd.* FILEthe name of the file on which to output these quantities=sphere_restraint.dat STRIDE the frequency with which the quantities of interest should be output=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ref_coord.x,ref_coord.y,ref_coord.z FILEthe name of the file on which to output these quantities=ref_coord.dat STRIDE the frequency with which the quantities of interest should be output=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=AR6_coord.x,AR6_coord.y,AR6_coord.z FILEthe name of the file on which to output these quantities=AR6_coord.dat STRIDE the frequency with which the quantities of interest should be output=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho,siga,theta 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=5000 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=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd FILEthe name of the file on which to output these quantities=rmsd.dat STRIDE the frequency with which the quantities of interest should be output=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=Dis FILEthe name of the file on which to output these quantities=distance.dat STRIDE the frequency with which the quantities of interest should be output=5000 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=5000