diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index bababa50c59e..125283589aef 100644
--- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -63,6 +63,12 @@ in stdenv.mkDerivation rec {
      ]
   ) ++ lib.optional enableCuda "-DGMX_GPU=CUDA";
 
+  postFixup = ''
+    substituteInPlace "$out"/lib/pkgconfig/*.pc \
+      --replace '=''${prefix}//' '=/' \
+      --replace "$out/$out/" "$out/"
+  '';
+
   meta = with lib; {
     homepage = "http://www.gromacs.org";
     license = licenses.gpl2;