Add note for COM removal with position restraints

Center of mass motion removal in combination with position restraints
will often cause artifacts. We should (automatically) disable this,
but this will disrupt workflows, so for now grompp will issue a note.

Refs #3244

Change-Id: If983e918d26f0af2fab96d44d0f2b1fc3cedb901

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index d6dbbe240cc215fe0462b9a06553d53c807ee83d..35f663a8f40e34f9900fc9c59f36bddd54830749 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -3863,12 +3863,12 @@ static void check_disre(const gmx_mtop_t* mtop)
     }
 }
 
-static bool absolute_reference(t_inputrec* ir, gmx_mtop_t* sys, bool posres_only, ivec AbsRef)
+static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t* sys, const bool posres_only, ivec AbsRef)
 {
     int                  d, g, i;
     gmx_mtop_ilistloop_t iloop;
     int                  nmol;
-    t_iparams*           pr;
+    const t_iparams*     pr;
 
     clear_ivec(AbsRef);
 
@@ -4086,6 +4086,13 @@ void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_
 
     set_warning_line(wi, mdparin, -1);
 
+    if (absolute_reference(ir, sys, false, AbsRef))
+    {
+        warning_note(wi,
+                     "Removing center of mass motion in the presence of position restraints might "
+                     "cause artifacts");
+    }
+
     if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 && ir->nstlist > 1
         && ((EI_MD(ir->eI) || EI_SD(ir->eI)) && (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
     {