MATLAB Examples

# write_gro_traj.m

• This function writes a .gro trajectory
• I think this function works...currently no support for printing velocities, see line 31
• Tested 15/07/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• write_gro_traj(atom,traj,Box_dim,filename_out)
```function write_gro_traj(atom,traj,Box_dim,filename_out) if regexp(filename_out,'.gro') ~= false; filename_out = filename_out; else filename_out = strcat(filename_out,'.gro'); end Frames=size(traj,1); nFrames=1:Frames; nAtoms=size(atom,2); Atom_section=cell(nAtoms,10); fid = fopen(filename_out, 'W'); tic for t=1:length(nFrames) t Title='.gro traj generated by matlab, t='; TitleTot={Title t}; fprintf(fid,'%-40s%10.5f \n',TitleTot{:}); fprintf(fid, '%-5i\n',nAtoms); % if isnan(atom(1).vx) || atom(1).vx == 0 for i = 1:nAtoms Atom_section(i,1:7) = [atom(i).molid, atom(i).resname, atom(i).type, atom(i).index, traj(t,1+3*(i-1))/10, traj(t,2+3*(i-1))/10, traj(t,3+3*(i-1))/10]; fprintf(fid, ']%-5s%5s]%8.3f%8.3f%8.3f\n', Atom_section{i,1:7}); end % else % disp('Currently no support for printing velocities') % pause % for i = 1:nAtoms % atom(i).molid % atom(i).resname % atom(i).type % atom(i).index % traj(t,1+3*(i-1))/10 % atom(i).vx(t)/10 % Atom_section(1:10) = [atom(i).molid, atom(i).resname, atom(i).type, atom(i).index, traj(t,1+3*(i-1))/10, traj(t,2+3*(i-1))/10, traj(t,3+3*(i-1))/10, atom(i).vx(t)/10, atom(i).vy(t)/10, atom(i).vz(t)/10]; % fprintf(fid, ']%-5s%5s]%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n', Atom_section{1:10}); % end % end if size(Box_dim,1)==1 if size(Box_dim,2) == 3 || Box_dim(4) == 0 && Box_dim(5) == 0 && Box_dim(6) == 0 fprintf(fid, '%10.5f%10.5f%10.5f\n',Box_dim(1:3)/10); else fprintf(fid, '%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n',Box_dim/10); end else if size(Box_dim(t,:),2) == 3 fprintf(fid, '%10.5f%10.5f%10.5f\n',Box_dim(t,1:3)/10); elseif Box_dim(t,4) == 0 && Box_dim(t,5) == 0 && Box_dim(t,6) == 0 fprintf(fid, '%10.5f%10.5f%10.5f\n',Box_dim(t,1:3)/10); else fprintf(fid, '%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n',Box_dim(t,:)/10); end end if mod(t,10)==0 t end end toc fclose(fid); sprintf('.gro file exported %d frames', nFrames(end)) ```