List of topology functions
Contents
Version
2.11
Contact
Please report problems/bugs to michael.holmboe@umu.se
Custom toplogy tools
Clayff, with atomtypes by MHolmboe
- charge_atom(atom,Box_dim,ffname,watermodel,varargin) % This function tries to charge the atom accorind to clayff or interface ff
- charge_clayff_2004_atom(atom,Box_dim,varargin) % Sets the charge for the original Clayff atomtypes for the original Clayff ff from the Cygan et al., 2004 paper
- charge_clayff_atom(atom,Box_dim,varargin) % Sets the charge for Clayff atomtypes
- charge_opls_go_atom(atom,Box_dim,varargin) % Sets the charge for some specific OPLS atomtypes
- check_clayff_2004_charge(atom) % check_clayff_2004_charge.m - This checks the charge of the original Clayff atomtypes by Mholmboe
- check_clayff_charge(atom) % check_clayff_charge.m - This checks the charge of the Clayff atomtypes by Mholmboe
- check_clayff_H2Odens(atom,Box_dim) % Check the approx. water density for a clayff system
- check_H2Odens(atom,Box_dim) % Computes the water density
- clayff_2004_atom(atom,Box_dim,varargin) % Assigns the original Clayff atom types by Cygan et al., 2004. Can also 'heal' edges
- clayff_2004_param(Atom_label,varargin) % Holds the ion and the original Clayff atomtype parameters
- clayff_atom(atom,Box_dim,varargin) % Assigns the Clayff atom types by MHolmboe. Can also 'heal' edges
- clayff_param(Atom_label,varargin) % Holds the ion and Clayff atomtype parameters
- clayffmod_atom(atom,Box_dim,varargin) % Assigns the modififed Clayff atom types. Can also 'heal' edges
- clayffmod_atom(atom,Box_dim,varargin) % New faster version. Assigns the modififed Clayff atom types. Can also 'heal' edges
- tweak_charge_atom(atom) % This function tries to tweak the charge of the atom struct in case of rounding errors
INTERFACE from Heinz 2005, 2013, with atomtypes by MHolmboe
- charge_atom(atom,Box_dim,ffname,watermodel,varargin) % This function tries to charge the atom accorind to clayff or interface ff
- interface_atom(atom,Box_dim,varargin) % This function tries to assign all atoms according to the interface atom types (with modified atom names by MHolmboe), with some modifications for edges...
- interface_param(Atom_label,water_model) % This holds the extended INTERFACE ff parameters
- interface15_atom(atom,Box_dim,varargin) % This function tries to assign all atoms according to the interface1.5 atom types (with modified atom names by MHolmboe), with some modifications for edges...
- interface15_param(Atom_label,water_model) % This holds the extended INTERFACE1.5 ff parameters
- charge_interface_atom(atom,Box_dim,varargin) % Sets the charge for Interface atomtypes
- charge_interface15_atom(atom,Box_dim,varargin) % Sets the charge for Interface 1.5 atomtypes
- check_interface_charge(atom) % This checks the charge of the INTERFACE atomtypes by Mholmboe
- check_interface15_charge(atom) % This checks the charge of the INTERFACE 1.5 atomtypes by Mholmboe
- tweak_charge_atom(atom) % This function tries to tweak the charge of the atom struct in case of rounding errors
Graphene oxide modeled with OPLS/aa stuff
- opls_go_atom(atom,Box_dim,rmin,rlarge) % This function tries to smear out the charge at around -OH and epoxides in GO
- oplsaa_go_param(Atom_label,water_model) % This custom function holds the extended oplsaa_aa ff for graphite oxide
- charge_opls_go_atom(atom,Box_dim,varargin) % Sets the charge for some specific OPLS atomtypes
Writing of topology files for Lammps (Clayff) and Gromacs (Clayff/INTERFACE)
- write_atom_all(atom,Box_dim,filename_out,varargin) % This function tries to write various files for you. Works best for systems designed for Clayff...
- write_atom_itp(atom,Box_dim,filename_out,varargin) % This script creates and prints a gromacs .itp file. Works best for clayff or interface ff with spc, spce or tip3p
- write_atom_lmp(atom,Box_dim,filename_out,varargin) % This script creates and prints a lammps data file (.lj). Works best for Clayff(_2004) systems
- write_atom_oplsaa_go_itp(atom,Box_dim,filename_out,varargin) % This custom made script creates and prints a gromacs .itp file for
- write_atom_psf(atom,Box_dim,filename_out,varargin) % This function writes an .psf file from the atom struct
%
Version
2.11
Contact
Please report problems/bugs to michael.holmboe@umu.se