Project ID: plumID:19.017
Source: plumed_metad/metad_20ang.dat
Originally used with PLUMED version: 2.5
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=1-2593 ENTITY1the atoms that make up a molecule that you wish to align=2594-2605 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=../input/heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL # 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)=../input/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H 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)=../input/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=sphere bnz: 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)=../input/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=BNZ_noH WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=bnz AROUNDreference atoms=sph 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 bnz_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=bnz sph_coord: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=sph_center NOPBC ignore the periodic boundary conditions when calculating distances bnz_coord: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=bnz_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=bnz_coord.x,sph_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=bnz_coord.y,sph_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=bnz_coord.z,sph_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 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 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=abs_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=abs_x,abs_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 # Restraining potential of the sphere restr: 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=2.0 KAPPAthe force constant for the wall=10000 # Coordination number c: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=bnz 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,theta,phi GRID_MINthe lower bounds for the grid=0,0.,-pi GRID_MAXthe upper bounds for the grid=2.2,pi,pi SIGMAthe widths of the Gaussian hills=0.1,pi/16.,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=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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho 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=500 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=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=restr.* 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=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=abs_x,abs_y,abs_z FILEthe name of the file on which to output these quantities=xyz_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=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 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