diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py
index a3bd668ea89..aaa5529db50 100644
--- a/var/spack/repos/builtin/packages/namd/package.py
+++ b/var/spack/repos/builtin/packages/namd/package.py
@@ -111,7 +111,7 @@ def _edit_arch_generic(self, spec, prefix):
                 else:
                     optims_opts = {
                         'gcc': m64 + '-O3 -fexpensive-optimizations \
-                                        -ffast-math ' + archopt,
+                                        -ffast-math -lpthread ' + archopt,
                         'intel': '-O2 -ip ' + archopt,
                         'aocc': m64 + '-O3 -ffp-contract=fast \
                                         -ffast-math ' + archopt}
@@ -226,7 +226,7 @@ def edit(self, spec, prefix):
             self._append_option(opts, 'cuda')
             filter_file('^CUDADIR=.*$',
                         'CUDADIR={0}'.format(spec['cuda'].prefix),
-                        self.arch + '.cuda')
+                        join_path('arch', self.arch + '.cuda'))
 
         config = Executable('./config')