MATLAB Examples

# write_atom_multiple_gro.m

• This function writes a .gro trajectory
• I think this function works...currently no support for printing velocities, see line 31
• Tested 15/04/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• write_atom_multiple_gro(atom,traj,filename_out)
```function write_atom_multiple_gro(atom,traj,filename_out) ```
```nFrames=[1:size(atom(1).x,1)]; nAtoms=size(atom,2); Atom_section=cell(nAtoms,10); fid = fopen(strcat(filename_out,'.gro'), 'W'); tic for frame=1:length(nFrames) Box_dim=traj.box(frame,:); Title='Generated by matlab t='; TitleTot={Title traj.time(frame)}; fprintf(fid,'%-40s%10.5f\n',TitleTot{:}); fprintf(fid,'%5i\n',nAtoms); %sprintf('.gro file imported %d frames', nFrames(end)) if isnan(atom(1).vx) || atom(1).vx == 0; %totstring=char(zeros(1,nAtoms*45)); for i = 1:nAtoms Atom_section(1:7) = [atom(i).molid, atom(i).resname, atom(i).type, atom(i).index, atom(i).x(frame)/10, atom(i).y(frame)/10, atom(i).z(frame)/10]; %string=sprintf(']%-5s%5s]%8.3f%8.3f%8.3f\n', Atom_section{1:7}); %totstring=[totstring string]; fprintf(fid, ']%-5s%5s]%8.3f%8.3f%8.3f\n', Atom_section{1:7}); end %fprintf(fid,'%s%\n',totstring); %size(totstring); else % Untested for i = 1:nAtoms Atom_section(1:10) = [atom(i).molid, atom(i).resname, atom(i).type, atom(i).index, atom(i).x(frame)/10, atom(i).y(frame)/10, atom(i).z(frame)/10, atom(i).vx(frame)/10, atom(i).vy(frame)/10, atom(i).vz(frame)/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,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 if mod(frame,10)==0; frame end end toc fclose(fid); sprintf('.gro file exported %d frames', nFrames(end)) ```