set_pull_init(ir,sys,state.x,state.box,oenv,opts->pull_start);
if (ir->bRot)
- set_reference_positions(ir->rot,sys,state.x,state.box,opt2fn("-ref",NFILE,fnm),wi);
+ {
+ set_reference_positions(ir->rot,sys,state.x,state.box,
+ opt2fn("-ref",NFILE,fnm),opt2bSet("-ref",NFILE,fnm),
+ wi);
+ }
/* reset_multinr(sys); */