List<String> renameCommand = gromacsRun.make_ndx(command,
selectionCommand, groupName);
command = GromacsCommandBuilder.getInstance()
.createMakeNdxRenameCommand(frame.getGTab().getFilePath(),
frame.getGTab().getProjectLocation(), fileName);
gromacsRun.renameNdxGroup(command, renameCommand);
} catch (IOException e) {
JOptionPane.showMessageDialog(frame, e.getMessage(), "Run error",
JOptionPane.ERROR_MESSAGE);
e.printStackTrace();