Project ID: plumID:23.025
Source: cylinder_metadynamics/3ibk/terra_metady_cyl_K1.dat
Originally used with PLUMED version: 2.7
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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UNITSThis command sets the internal units for the code. More detailsLENGTH=A # modify the default length unit (nm) to Angstrom and energy to kcal/molthe units of lengthsWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-1520,35634 # atoms of receptor and ligandthe atoms that make up a molecule that you wish to alignFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsREFERENCE=3ibk_tetradcore.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL # pdb with reference atoms to fitthe manner in which RMSD alignment is performed
#######################################3 # Defining groups and binding site Klig: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 detailsATOMS=35634 # K bulk ion that will serve as ligand K1:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=1517 # K1 ion that will serve as binding site reference K2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=1519 # K2 ion that will serve as binding site referencethe numerical indexes for the set of atoms in the group
tetrad1: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 detailsATOMS=132-161,511-540,890-919,1269-1298 # GUA base atoms tetrad2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=198-227,577-606,956-985,1335-1364 # GUA base atoms tetrad3:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=264-293,643-672,1022-1051,1401-1430 # GUA base atomsthe numerical indexes for the set of atoms in the group
site1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=tetrad3,tetrad2 # region of K1 ion that will serve as binding site reference site2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=tetrad1,tetrad2 # region of K2 ion that will serve as binding site referencethe list of atoms which are involved the virtual atom's definition
KBULK: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 detailsATOMS=35596,35598,35600,35602,35604,35606,35608,35610,35612,35614,35616,35618,35620,35622,35624,35626,35628,35630,35632,35636,35638,35640,35642,35644,35646,35648,35650,35652,35654 # K bulk ionsthe numerical indexes for the set of atoms in the group
check_site1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=K1,site1 check_site2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=K2,site2the pair of atom that we are calculating the distance betweenWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More detailsATOMS=Kligwrapped atomsAROUND=tetrad1,tetrad2,tetrad3reference atoms
####################################### # Creating KBULK binding restraints to K1 and K2 # to prevent ion binding competition
mindist1:DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=K1Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=KBULKCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLOWESTrepulsivewall1:this flag allows you to recover the lowest of these variablesLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=mindist1.lowestthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0the offset for the start of the wall
mindist2:DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More detailsGROUPA=K2Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=KBULKCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLOWESTrepulsivewall2:this flag allows you to recover the lowest of these variablesLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=mindist2.lowestthe arguments on which the bias is actingAT=6.0the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0the offset for the start of the wall
####################################### # Build the cylinder using site1 and Klig coordinates
Klig_coord:POSITIONCalculate the components of the position of an atom. More detailsATOM=Kligthe atom numberNOPBCsite1_coord:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=site1the atom numberNOPBCignore the periodic boundary conditions when calculating distances
# calculating the distance from site1 to Klig d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=Klig,site1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as label
# distances for each cartesian component abs_x:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=Klig_coord.x,site1_coord.xthe values input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NO abs_y:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=Klig_coord.y,site1_coord.ythe values input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NO abs_z:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=Klig_coord.z,site1_coord.zthe values input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Defining cylinder via descriptive coordinates rho:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_x,abs_ythe values input to this functionFUNC=sqrt(x*x+y*ythe function you wish to evaluatePERIODIC=NO phi:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_x,abs_ythe values input to this functionFUNC=atan2(y,xthe function you wish to evaluatePERIODIC=-pi,piif the output of your function is periodic then you should specify the periodicity of the function
# restraining cylinder lateral size cylrestr1:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rhothe arguments on which the bias is actingAT=7.0the positions of the wallKAPPA=5000 # controls the maximum cylinder radius - 0.7 nm in this casethe force constant for the wall
# restraining K1 from transpassing the cylinder heights cylrestr2:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1.zthe arguments on which the bias is actingAT=1.5the positions of the wallKAPPA=2500 # controls the maximum cylinder height. IMPORTANT - this must be a LOWER_WALLs if your binding site is at a negative Z region cylrestr3:the force constant for the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1.zthe arguments on which the bias is actingAT=22.0the positions of the wallKAPPA=2500 # controls the minimum cylinder height. IMPORTANT - this must be a UPPER_WALLs if your binding site is at a negative Z regionthe force constant for the wall
######################################## # Defining CV and metadynamics procedures
d1real:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=Klig,K1 d1real_xyz:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=Klig,K1the pair of atom that we are calculating the distance betweenCOMPONENTScalculate the x, y and z components of the distance separately and store them as label
thetax:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_x,d1realthe values input to this functionFUNC=asin(x/y)*(180/pithe function you wish to evaluatePERIODIC=NO thetay:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_y,d1realthe values input to this functionFUNC=asin(x/y)*(180/pithe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
metad:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=d1.z,rho,phithe labels of the scalars on which the bias will actSIGMA=0.5,0.5,pi/8the widths of the Gaussian hillsHEIGHT=1.0the heights of the Gaussian hillsPACE=500the frequency for hill additionFILE=HILLS_CYLa file in which the list of added hills is storedGRID_MIN=0.0,0.0,-pithe lower bounds for the gridGRID_MAX=25.0,10.0,pithe upper bounds for the gridBIASFACTOR=5use well tempered metadynamics and use this bias factorCALC_RCTcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]TEMP=298the system temperature - this is only needed if you are doing well-tempered metadynamics
######################################## # Printing argumentsPrint quantities to a file. More detailsARGthe labels of the values that you would like to print to the fileSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=COLVAR_CYLthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=d1.z,d1real,d1real_xyz.zthe labels of the values that you would like to print to the fileFILE=distance.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=metadthe labels of the values that you would like to print to the fileFILE=metad_data.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=cylrestr1.*,cylrestr2.*,cylrestr3the labels of the values that you would like to print to the fileFILE=cylinder_restraint.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=mindist1.lowest,repulsivewall1.*,mindist2.lowest,repulsivewall2the labels of the values that you would like to print to the fileFILE=repulsivewalls.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=abs_x,abs_y,abs_zthe labels of the values that you would like to print to the fileFILE=xyz_coord.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=rho,d1.z,phithe labels of the values that you would like to print to the fileFILE=rdp_coord.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=thetax,thetaythe labels of the values that you would like to print to the fileFILE=angles.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=check_site1,check_site2the labels of the values that you would like to print to the fileFILE=check_site.datthe name of the file on which to output these quantitiesSTRIDE=1000the frequency with which the quantities of interest should be outputDUMPATOMSDump selected atoms on a file. More detailsSTRIDE=1000the frequency with which the atoms should be outputFILE=lig_coords.grofile on which to output coordinates; extension is automatically detectedATOMS=Kligthe atom indices whose positions you would like to print outFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushed