XTCReporter overwrites existing xtc file (#4657)

* XTCReporter overwrite existing xtc file

* add position size check for xtcfile

wrappers/python/openmm/app/xtcfile.py

@@ -99,6 +99,8 @@ class XTCFile(object):
             raise ValueError(
                 "Particle position is infinite.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan"
             )
+        if (np.abs(positions * 1000) > (2 ** 31 - 1)).any():
+            raise ValueError("Particle position is too large for XTC format")
 
         self._modelCount += 1
         if (

wrappers/python/openmm/app/xtcreporter.py

@@ -29,6 +29,8 @@ class XTCReporter(object):
         self._enforcePeriodicBox = enforcePeriodicBox
         self._fileName = file
         self._xtc = None
+        if not append:
+            open(file, 'wb').close()
 
     def describeNextReport(self, simulation):
         """Get information about the next report this object will generate.