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
tested onv2.10
tested onmaster
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A # modify the default length unit (nm) to Angstrom and energy to kcal/mol

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=1-1520,35634 # atoms of receptor and ligand 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=3ibk_tetradcore.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL # pdb with reference atoms to fit
#######################################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 details ATOMSthe numerical indexes for the set of atoms in the group=35634 # K bulk ion that will serve as ligand K1: 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=1517 # K1 ion that will serve as binding site reference K2: 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=1519 # K2 ion that will serve as binding site reference
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 details ATOMSthe numerical indexes for the set of atoms in the group=132-161,511-540,890-919,1269-1298 # GUA base atoms tetrad2: 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=198-227,577-606,956-985,1335-1364 # GUA base atoms tetrad3: 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=264-293,643-672,1022-1051,1401-1430 # GUA base atoms
site1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tetrad3,tetrad2 # region of K1 ion that will serve as binding site reference site2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=tetrad1,tetrad2 # region of K2 ion that will serve as binding site reference
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 details ATOMSthe numerical indexes for the set of atoms in the group=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 ions
check_site1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=K1,site1 check_site2: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=K2,site2 WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=Klig AROUNDreference atoms=tetrad1,tetrad2,tetrad3 ####################################### # 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 details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=KBULK LOWEST this flag allows you to recover the lowest of these variables repulsivewall1: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=mindist1.lowest ATthe positions of the wall=6.0 KAPPAthe force constant for the wall=2000.0 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 mindist2: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=KBULK LOWEST this flag allows you to recover the lowest of these variables repulsivewall2: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=mindist2.lowest ATthe positions of the wall=6.0 KAPPAthe force constant for the wall=2000.0 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 ####################################### # Build the cylinder using site1 and Klig coordinates
Klig_coord: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=Klig NOPBC ignore the periodic boundary conditions when calculating distances site1_coord: POSITIONCalculate the components of the position of an atom. More details ATOMthe atom number=site1 NOPBC ignore the periodic boundary conditions when calculating distances
# calculating the distance from site1 to Klig d1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=Klig,site1 COMPONENTS calculate 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 details ARGthe values input to this function=Klig_coord.x,site1_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=Klig_coord.y,site1_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=Klig_coord.z,site1_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 # 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 details ARGthe values input to this function=abs_x,abs_y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 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 cylinder lateral size cylrestr1: 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=7.0 KAPPAthe force constant for the wall=5000 # controls the maximum cylinder radius - 0.7 nm in this case
# restraining K1 from transpassing the cylinder heights cylrestr2: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=1.5 KAPPAthe force constant for the wall=2500 # controls the maximum cylinder height. IMPORTANT - this must be a LOWER_WALLs if your binding site is at a negative Z region cylrestr3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=22.0 KAPPAthe force constant for the wall=2500 # controls the minimum cylinder height. IMPORTANT - this must be a UPPER_WALLs if your binding site is at a negative Z region
######################################## # Defining CV and metadynamics procedures
d1real: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=Klig,K1 d1real_xyz: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=Klig,K1 COMPONENTS calculate 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 details ARGthe values input to this function=abs_x,d1real FUNCthe function you wish to evaluate=asin(x/y)*(180/pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO thetay: 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,d1real FUNCthe function you wish to evaluate=asin(x/y)*(180/pi) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO metad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=d1.z,rho,phi SIGMAthe widths of the Gaussian hills=0.5,0.5,pi/8. HEIGHTthe heights of the Gaussian hills=1.0 PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=HILLS_CYL GRID_MINthe lower bounds for the grid=0.0,0.0,-pi GRID_MAXthe upper bounds for the grid=25.0,10.0,pi BIASFACTORuse well tempered metadynamics and use this bias factor=5 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 ######################################## # Printing arguments PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR_CYL PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.z,d1real,d1real_xyz.z 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=1000 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=1000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cylrestr1.*,cylrestr2.*,cylrestr3.* FILEthe name of the file on which to output these quantities=cylinder_restraint.dat STRIDE the frequency with which the quantities of interest should be output=1000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=mindist1.lowest,repulsivewall1.*,mindist2.lowest,repulsivewall2.* FILEthe name of the file on which to output these quantities=repulsivewalls.dat STRIDE the frequency with which the quantities of interest should be output=1000 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=1000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rho,d1.z,phi FILEthe name of the file on which to output these quantities=rdp_coord.dat STRIDE the frequency with which the quantities of interest should be output=1000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=thetax,thetay FILEthe name of the file on which to output these quantities=angles.dat STRIDE the frequency with which the quantities of interest should be output=1000 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=check_site1,check_site2 FILEthe name of the file on which to output these quantities=check_site.dat STRIDE the frequency with which the quantities of interest should be output=1000 DUMPATOMSDump selected atoms on a file. More details STRIDE the frequency with which the atoms should be output=1000 FILEfile on which to output coordinates; extension is automatically detected=lig_coords.gro ATOMSthe atom indices whose positions you would like to print out=Klig 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=1000