Added flat-bottom cylindrical restraints in x and y.

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / readir.c

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 7fcd21cd9f92c25ea1cd5faafe938c1793414ccd..0322b5b28c490ee4807eb4a3d05f38fd8234d28e 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -36,8 +36,6 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <ctype.h>
 #include <limits.h>
 #include <stdlib.h>
@@ -371,6 +369,11 @@ void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
             warning_error(wi, warn_buf);
         }
 
+        if (ir->implicit_solvent != eisNO)
+        {
+            warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
+        }
+
         if (ir->nstlist <= 0)
         {
             warning_error(wi, "With Verlet lists nstlist should be larger than 0");
@@ -1332,11 +1335,9 @@ nd %s",
     /* IMPLICIT SOLVENT */
     if (ir->coulombtype == eelGB_NOTUSED)
     {
-        ir->coulombtype      = eelCUT;
-        ir->implicit_solvent = eisGBSA;
-        fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
-                "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
-                "setting implicit-solvent value to \"GBSA\" in input section.\n");
+        sprintf(warn_buf, "Invalid option %s for coulombtype",
+                eel_names[ir->coulombtype]);
+        warning_error(wi, warn_buf);
     }
 
     if (ir->sa_algorithm == esaSTILL)
@@ -3822,7 +3823,15 @@ static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
                         case efbposresSPHERE:
                             AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
                             break;
+                        case efbposresCYLINDERX:
+                            AbsRef[YY] = AbsRef[ZZ] = 1;
+                            break;
+                        case efbposresCYLINDERY:
+                            AbsRef[XX] = AbsRef[ZZ] = 1;
+                            break;
                         case efbposresCYLINDER:
+                        /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
+                        case efbposresCYLINDERZ:
                             AbsRef[XX] = AbsRef[YY] = 1;
                             break;
                         case efbposresX: /* d=XX */