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
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
mindist1DISTANCESCalculate 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 mindist2DISTANCESCalculate 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