Merge branch 'master' into rotation

[alexxy/gromacs.git] / src / kernel / grompp.c

diff --git a/src/kernel/grompp.c b/src/kernel/grompp.c
index 48353f6e70f6e339c93ba3a7e44356f011564938..72efea555fdc5b0941eddad56fe7f907048b7078 100644 (file)
--- a/src/kernel/grompp.c
+++ b/src/kernel/grompp.c
@@ -1208,7 +1208,8 @@ int main (int argc, char *argv[])
     { efTOP, "-pp", "processed", ffOPTWR },
     { efTPX, "-o",  NULL,        ffWRITE },
     { efTRN, "-t",  NULL,        ffOPTRD },
-    { efEDR, "-e",  NULL,        ffOPTRD }
+    { efEDR, "-e",  NULL,        ffOPTRD },
+    { efTRN, "-ref","rotref",    ffOPTRW }
   };
 #define NFILE asize(fnm)
 
@@ -1482,6 +1483,9 @@ int main (int argc, char *argv[])
 
   if (ir->ePull != epullNO)
     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);
 
   /*  reset_multinr(sys); */