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
tested onv2.10
tested onmaster
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