remove_SOL.m

This function removes water molecules between the lo and hi limits
along the dim dimension. Does it work for tip4p and tip5p water?
Untested for quite some time

Version
Contact
Examples

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

Examples

atom = remove_SOL(atom,atomname,0,10,'z')
atom = remove_SOL(atom,atomname,0,10,'z','OW')

function atom = remove_SOL(atom,atomname,lo,hi,dim,varargin)

nAtoms=size(atom,2);

ind=find(strncmpi([atom.type],atomname,2));

if strcmp(dim,'x')
    atomcoords=[atom.x];
elseif strcmp(dim,'y')
    atomcoords=[atom.y];
elseif strcmp(dim,'z')
    atomcoords=[atom.z];
end

ind_lo=find(atomcoords>lo);ind_lo=intersect(ind_lo,ind);
ind_hi=find(atomcoords<hi);ind_hi=intersect(ind_hi,ind);
ind=intersect(ind_lo,ind_hi);
if strncmpi(atomname,'OW',2)
    ind_HW1=ind+1;ind_HW2=ind+2;
    ind=sort([ind ind_HW1 ind_HW2]);
end

if nargin == 6
    if strncmpi(atomname,'OW',2)
        nrmSOL=3*cell2mat(varargin(1));
    else
        nrmSOL=cell2mat(varargin(1));
    end
else
    nrmSOL=length(ind);
end

length(ind)

ind=ind(1:nrmSOL);

change_ind=sort(setdiff(1:nAtoms,ind));
atom=atom(change_ind);
atom=update_atom(atom);

% %

remove_SOL.m

Contents

Version

Contact

Examples