From a99873a8fe83bef0169341bd0471e33946f4396f Mon Sep 17 00:00:00 2001
From: Felix Pultar <felix.pultar@phys.chem.ethz.ch>
Date: Tue, 17 Oct 2023 17:02:44 +0200
Subject: [PATCH] fix in gromosPP

Signed-off-by: Felix Pultar <felix.pultar@phys.chem.ethz.ch>
---
 pygromos/gromos/gromosPP.py | 19 ++++++++++---------
 pygromos/utils/bash.py      |  1 +
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/pygromos/gromos/gromosPP.py b/pygromos/gromos/gromosPP.py
index 3359747e..982a9e7b 100644
--- a/pygromos/gromos/gromosPP.py
+++ b/pygromos/gromos/gromosPP.py
@@ -931,7 +931,7 @@ def ran_box(
         in_cnf_path: str,
         out_cnf_path: str = "",
         periodic_boundary_condition: str = "r",
-        nmolecule: int = 1,
+        nmolecule: str = "1",
         dens: float = 1.0,
         threshold: float = None,
         layer: bool = False,
@@ -972,21 +972,21 @@ def ran_box(
             + " @pos "
             + in_cnf_path
             + " @nsm "
-            + str(nmolecule)
+            + nmolecule
             + " @dens "
             + str(dens)
             + " "
             + command_suffix
             + " > "
             + out_cnf_path
-            + " \n"
         )
-        if not return_command_only:
-            print(command)
-            bash.execute(command, verbose=verbose)
-            return out_cnf_path
-        else:
-            return command
+
+
+        p = bash.execute(command, verbose=verbose)
+        if verbose:
+            print(p.stdout)
+            print(p.stderr)
+        return out_cnf_path
 
     @_gromosClass._gromosTypeConverter
     def build_box(
@@ -1131,6 +1131,7 @@ def red_top(self, in_top_path: str, atom_selection: str, out_top_path: str, _bin
             "> " + out_top_path + " \n",
         ]
         bash.execute(command)
+
         return out_top_path
 
     @_gromosClass._gromosTypeConverter
diff --git a/pygromos/utils/bash.py b/pygromos/utils/bash.py
index 0e25a257..d831d551 100644
--- a/pygromos/utils/bash.py
+++ b/pygromos/utils/bash.py
@@ -810,6 +810,7 @@ def execute_subprocess(
         env = os.environ.copy()
 
     p = sub.Popen(args=command, shell=True, stderr=sub.PIPE, env=env, **kwargs)
+    out, err = p.communicate()
 
     # print(p, vars(p))
     try: