Fix file open (#188)

* Fixed #181 
* Added change for capture_output_file arg fix
* update CHANGES

CHANGES

@@ -3,8 +3,10 @@
 ==============================
 
 2020-xx-xx     0.8.1
-orbeckst, PolyachenkoYA 
+orbeckst, PolyachenkoYA, whitead 
 
+* fixed: core._run_command capture_output_file argument fixed to us python-3.0 
+  file open (#181)
 * fixed: xvg._decimate used python-2.0-specific func_name() (issue #183)
 * fixed: make parsing gmx output more robust to avoid failure on 
   'import gromacs' (PR #186)

gromacs/core.py

@@ -207,7 +207,7 @@ def _run_command(self, *args, **kwargs):
             else:
                 # XXX: not race or thread proof; potentially many commands write to the same file
                 fn = environment.flags['capture_output_filename']
-                capturefile = file(fn, "w")   # overwrite (clobber) capture file
+                capturefile = open(fn, "w")   # overwrite (clobber) capture file
                 if 'stdout' in kwargs and 'stderr' not in kwargs:
                     # special case of stdout used by code but stderr should be captured to file
                     kwargs.setdefault('stderr', capturefile)