Project ID: plumID:25.020
Source: apoADRB1_NA/3/plumed_pNA_Z.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
#SETTINGS NATOMS=2000000 #RESTART
p1: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=final_path.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=90.71 uwallZ: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.zzz ATthe positions of the wall=0.15 KAPPAthe force constant for the wall=2500.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 lwallS: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.sss ATthe positions of the wall=1.3 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 szparab: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,p1.zzz FUNCthe function you wish to evaluate=y+(0.00111*(x-7)^2)-0.05 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO uwallsz: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=szparab ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=200000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 r3: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=7bts_soloCA_fix.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL r4: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=inactive_state.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL #PIF SC94: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1438,1440,1444,1447 SC184: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=2885,2888,2891 SC227: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3613,3616,3617,3619,3621,3623,3625 d94-184: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC94,SC184 d94-227: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC94,SC227 d184-227: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC184,SC227 PIF1-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d94-184 FUNCthe function you wish to evaluate=y+(0.0045*(x^2))-1.22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PIF2-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d94-227 FUNCthe function you wish to evaluate=y+(0.0045*(x^2))-1.22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PIF3-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d184-227 FUNCthe function you wish to evaluate=y+(0.0045*(x^2))-1.45 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO uwallPIF: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=PIF1-path,PIF2-path,PIF3-path ATthe positions of the wall=0.0,0.0,0.0 KAPPAthe force constant for the wall=5000.0,5000.0,5000.0 EXP the powers for the walls=2,2,2 EPS the values for s_i in the expression for a wall=1,1,1 OFFSET the offset for the start of the wall=0,0,0 #NPxxY SC192: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3014,3017,3018,3020,3022,3023,3025,3027 SC271: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=4353,4356,4357,4359,4361,4362,4364,4366 SC267: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=4287,4290,4291,4292 SC52: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=418,419,420,421 d192-271: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC192,SC271 d192-267: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC192,SC267 d271-52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC271,SC52 d192-271-path: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=p1.sss,d192-271 FUNCthe function you wish to evaluate=y+(0.0045*(x^2))-1.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO uwallNPxxY: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d192-271-path ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 #YY WO: 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 ATOMSthe numerical indexes for the set of atoms in the group=41338-123566:4 #water oxygen atoms yycenter1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=4362,3512,1533 #IsoLeu100 Cb, Leu220 Cgamma, Tyr271 OH yywo: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=yycenter1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.30 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=50 con192: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC192 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC271 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.90 NN=8 MM=12} yywoprod: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=yywo,con192 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 yywosum: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=yywo,con192 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 #DRY SC114: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=956,957,958,959,960,961,962,963 SC103: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=856,857,858,859 SC104: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=865,866,867,868,869,870,871 SC213: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3390,3393,3396,3397,3398 SC108: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=905,906,907,908 SC217: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1792,1793,1794,1795 d103-114: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC103,SC114 d104-213: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC104,SC213 d108-217: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC108,SC217 NApoint1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1075,2596 NApoint2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1267,2608,1329,2590 NApoint3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1332,4137 NApoint4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1387,840,3680 NApoint5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=793,4232,1427,3680 NAghost: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=NApoint3,NApoint1,NApoint2 COORDINATEScoordinates of the ghost atom in the local reference frame=1.45,0.0,0.0 NApoint1NA3: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=NAghost GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=41264 MINcalculate the minimum value={BETA=10.} NApoint2NA3: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=NApoint1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=41264 MINcalculate the minimum value={BETA=10.} NApoint3NA3: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=NApoint2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=41264 MINcalculate the minimum value={BETA=10.} NApoint4NA3: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=NApoint3 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=41264 MINcalculate the minimum value={BETA=10.} NApoint5NA3: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=NApoint4 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=41264 MINcalculate the minimum value={BETA=10.} NApoint6NA3: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=NApoint5 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=41264 MINcalculate the minimum value={BETA=10.}
NaPATH: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=NApoint1NA3.min,NApoint2NA3.min,NApoint3NA3.min,NApoint4NA3.min,NApoint5NA3.min,NApoint6NA3.min VARthe names to give each of the arguments in the function=ax,bx,cx,dx,ex,fx FUNCthe function you wish to evaluate=((1*exp(-6*(ax*ax)))+(2*exp(-6*(bx*bx)))+(3*exp(-6*(cx*cx)))+(4*exp(-6*(dx*dx)))+(5*exp(-6*(ex*ex)))+(6*exp(-6*(fx*fx))))/((1*exp(-6*(ax*ax)))+(1*exp(-6*(bx*bx)))+(1*exp(-6*(cx*cx)))+(1*exp(-6*(dx*dx)))+(1*exp(-6*(ex*ex)))+(1*exp(-6*(fx*fx)))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO NaPATHL3: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=NApoint1NA3.min,NApoint2NA3.min,NApoint3NA3.min,NApoint4NA3.min,NApoint5NA3.min,NApoint6NA3.min VARthe names to give each of the arguments in the function=ax,bx,cx,dx,ex,fx FUNCthe function you wish to evaluate=((1*exp(-3*(ax*ax)))+(2*exp(-3*(bx*bx)))+(3*exp(-3*(cx*cx)))+(4*exp(-3*(dx*dx)))+(5*exp(-3*(ex*ex)))+(6*exp(-3*(fx*fx))))/((1*exp(-3*(ax*ax)))+(1*exp(-3*(bx*bx)))+(1*exp(-3*(cx*cx)))+(1*exp(-3*(dx*dx)))+(1*exp(-3*(ex*ex)))+(1*exp(-3*(fx*fx)))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO NaPATHZ: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=NApoint1NA3.min,NApoint2NA3.min,NApoint3NA3.min,NApoint4NA3.min,NApoint5NA3.min,NApoint6NA3.min VARthe names to give each of the arguments in the function=ax,bx,cx,dx,ex,fx FUNCthe function you wish to evaluate=-0.167*log(((1*exp(-6*(ax*ax)))+(1*exp(-6*(bx*bx)))+(1*exp(-6*(cx*cx)))+(1*exp(-6*(dx*dx)))+(1*exp(-6*(ex*ex)))+(1*exp(-6*(fx*fx))))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO uwallpNAZ: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=NaPATHZ ATthe positions of the wall=0.9 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 uwallpNA: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=NaPATH ATthe positions of the wall=5.8 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 d55-89: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=844,1379 d55-90: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=844,1387 d55combo: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d55-89,d55-90 VARthe names to give each of the arguments in the function=ax,bx FUNCthe function you wish to evaluate=ax+bx PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO NApoint5WO: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NApoint4WO: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NApoint3WO: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NApoint2WO: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NA5b: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO,41264 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NA4b: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO,41264 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NA3b: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=NApoint3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO,41264 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NA54b: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=NA5b,NA4b VARthe names to give each of the arguments in the function=ax,bx FUNCthe function you wish to evaluate=(ax/3.5)-(bx/3.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO NA34b: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=NA3b,NA4b VARthe names to give each of the arguments in the function=ax,bx FUNCthe function you wish to evaluate=(ax/3.5)-(bx/3.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO NaWater: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=NA54b,NA34b VARthe names to give each of the arguments in the function=ax,bx FUNCthe function you wish to evaluate=ax+bx PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ene: ENERGYCalculate the total potential energy of the simulation box. More details
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=opes ARGthe labels of the scalars on which the bias will act=p1.sss,NaPATHL3 SIGMA the initial widths of the kernels, divided by the square root of gamma=0.05,0.05 FILE a file in which the list of all deposited kernels is stored=Kernels.data # STATE_RFILE=compressed0.Kernels STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels PACEthe frequency for kernel deposition=50000 BARRIERthe free energy barrier to be overcome=100 RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO ... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=opese1 ARGthe labels of the scalars on which the bias will act=NaWater,yywosum SIGMA the initial widths of the kernels, divided by the square root of gamma=0.02,0.02 FILE a file in which the list of all deposited kernels is stored=Kernelse1.data # STATE_RFILE=compressed0.Kernelse1 STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernelse1 PACEthe frequency for kernel deposition=100000 BARRIERthe free energy barrier to be overcome=10 RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO ... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=opese2 ARGthe labels of the scalars on which the bias will act=d192-271,yywosum SIGMA the initial widths of the kernels, divided by the square root of gamma=0.02,0.02 FILE a file in which the list of all deposited kernels is stored=Kernelse2.data # STATE_RFILE=compressed0.Kernelse2 STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernelse2 PACEthe frequency for kernel deposition=100000 BARRIERthe free energy barrier to be overcome=3 RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO ... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=opese3 ARGthe labels of the scalars on which the bias will act=d192-267,yywosum SIGMA the initial widths of the kernels, divided by the square root of gamma=0.03,0.02 FILE a file in which the list of all deposited kernels is stored=Kernelse3.data # STATE_RFILE=compressed0.Kernelse3 STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernelse3 PACEthe frequency for kernel deposition=100000 BARRIERthe free energy barrier to be overcome=3 RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO ... OPES_METAD_EXPLORE
ecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=306 TEMP_STEPSthe number of steps in temperature=4 opesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details ARGthe label of the ECVs that define the expansion=ecv.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=10000 UPDATE_FROMOnly update this action from this time=5000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500