From b0b453cf81a22a4af89b4f5882a54e01d38fde57 Mon Sep 17 00:00:00 2001
From: MichaelShohat <38256261+MichaelShohat@users.noreply.github.com>
Date: Mon, 17 Jun 2019 00:06:14 +0300
Subject: [PATCH] latest debug sessoin

---
 environment.yml                               |  89 ++++++
 runtime.txt                                   |   1 +
 src/SimuMole/SimuMole/settings.py             |   2 +-
 .../SimuMoleScripts/basicTrajectoryBuilder.py |  69 ++--
 src/SimuMole/SimuMoleScripts/emailSender.py   |   4 +-
 .../SimuMoleScripts/simulation_main_script.py | 140 +++-----
 .../SimuMoleScripts/uploaded_simulation.py    |  35 +-
 src/SimuMole/SimuMoleWeb/forms.py             | 301 +++++++++---------
 .../templates/create_simulation.html          |  12 +-
 .../templates/create_simulation_result.html   |   5 +
 src/SimuMole/SimuMoleWeb/templates/home.html  |   2 +-
 src/SimuMole/SimuMoleWeb/views.py             |  72 ++---
 .../media/files/_init_folder_file.txt         |   1 -
 13 files changed, 405 insertions(+), 328 deletions(-)
 create mode 100644 environment.yml
 create mode 100644 runtime.txt
 delete mode 100644 src/SimuMole/media/files/_init_folder_file.txt

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..717852c
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,89 @@
+name: simumoleEnv
+channels:
+  - omnia
+  - conda-forge
+  - schrodinger
+  - defaults
+dependencies:
+  - apbs=1.5=h14c3975_3
+  - asn1crypto=0.24.0=py37_0
+  - blas=1.0=mkl
+  - ca-certificates=2019.3.9=hecc5488_0
+  - certifi=2019.3.9=py37_0
+  - cffi=1.12.3=py37h2e261b9_0
+  - chardet=3.0.4=py37_1
+  - cryptography=2.7=py37h72c5cf5_0
+  - dbus=1.13.6=h746ee38_0
+  - expat=2.2.6=he6710b0_0
+  - fftw3f=3.3.4=2
+  - fontconfig=2.13.0=h9420a91_0
+  - freemol=1.158=py37_1
+  - freetype=2.9.1=h8a8886c_1
+  - glew=2.0.0=0
+  - glib=2.56.2=hd408876_0
+  - gst-plugins-base=1.14.0=hbbd80ab_1
+  - gstreamer=1.14.0=hb453b48_1
+  - h5py=2.9.0=py37h7918eee_0
+  - hdf5=1.10.4=hb1b8bf9_0
+  - icu=58.2=h9c2bf20_1
+  - idna=2.8=py37_0
+  - intel-openmp=2019.4=243
+  - jpeg=9b=h024ee3a_2
+  - libedit=3.1.20181209=hc058e9b_0
+  - libffi=3.2.1=hd88cf55_4
+  - libgcc-ng=8.2.0=hdf63c60_1
+  - libgfortran-ng=7.3.0=hdf63c60_0
+  - libglu=9.0.0=hf484d3e_1
+  - libopenblas=0.3.6=h5a2b251_0
+  - libpng=1.6.37=hbc83047_0
+  - libstdcxx-ng=8.2.0=hdf63c60_1
+  - libtiff=4.0.10=h2733197_2
+  - libuuid=1.0.3=h1bed415_2
+  - libxcb=1.13=h1bed415_1
+  - libxml2=2.9.9=he19cac6_0
+  - mengine=1=h14c3975_1
+  - mkl=2019.4=243
+  - mkl_fft=1.0.12=py37ha843d7b_0
+  - mkl_random=1.0.2=py37hd81dba3_0
+  - mpeg_encode=1=h14c3975_1
+  - mtz2ccp4_px=1.0=h9ac9557_3
+  - ncurses=6.1=he6710b0_1
+  - numpy=1.16.4=py37h7e9f1db_0
+  - numpy-base=1.16.4=py37hde5b4d6_0
+  - olefile=0.46=py37_0
+  - openmm=7.3.1=py37_cuda92_rc_2
+  - openssl=1.1.1b=h14c3975_1
+  - pcre=8.43=he6710b0_0
+  - pdb2pqr=2.1.1=py37_1
+  - pdbfixer=1.5=py37_0
+  - pillow=6.0.0=py37h34e0f95_0
+  - pip=19.1.1=py37_0
+  - pmw=2.0.1=py37_2
+  - pycparser=2.19=py37_0
+  - pymol=2.3.2=py37h75f9260_0
+  - pyopenssl=19.0.0=py37_0
+  - pyqt=5.9.2=py37h05f1152_2
+  - pysocks=1.7.0=py37_0
+  - python=3.7.3=h0371630_0
+  - qt=5.9.7=h5867ecd_1
+  - readline=7.0=h7b6447c_5
+  - requests=2.22.0=py37_0
+  - rigimol=1.3=2
+  - setuptools=41.0.1=py37_0
+  - sip=4.19.8=py37hf484d3e_0
+  - six=1.12.0=py37_0
+  - sqlite=3.28.0=h7b6447c_0
+  - tk=8.6.8=hbc83047_0
+  - urllib3=1.24.2=py37_0
+  - wheel=0.33.4=py37_0
+  - xz=5.2.4=h14c3975_4
+  - zlib=1.2.11=h7b6447c_3
+  - zstd=1.3.7=h0b5b093_0
+  - pip:
+    - django==2.2.2
+    - django-formtools==2.1
+    - py3wetransfer==0.0.2
+    - python-magic==0.4.15
+    - pytz==2019.1
+    - sqlparse==0.3.0
+
diff --git a/runtime.txt b/runtime.txt
new file mode 100644
index 0000000..9955289
--- /dev/null
+++ b/runtime.txt
@@ -0,0 +1 @@
+Python 3.7.3
diff --git a/src/SimuMole/SimuMole/settings.py b/src/SimuMole/SimuMole/settings.py
index 0fd89c6..08df801 100644
--- a/src/SimuMole/SimuMole/settings.py
+++ b/src/SimuMole/SimuMole/settings.py
@@ -24,7 +24,7 @@
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True
 
-ALLOWED_HOSTS = []
+ALLOWED_HOSTS = ['marinemr135.quickbox.io', '176.9.8.180']
 
 # Application definition
 
diff --git a/src/SimuMole/SimuMoleScripts/basicTrajectoryBuilder.py b/src/SimuMole/SimuMoleScripts/basicTrajectoryBuilder.py
index 833b776..5702297 100644
--- a/src/SimuMole/SimuMoleScripts/basicTrajectoryBuilder.py
+++ b/src/SimuMole/SimuMoleScripts/basicTrajectoryBuilder.py
@@ -10,26 +10,29 @@
 traj_dcd = 'trajectory.dcd'
 
 
-def scr(input_coor_name, temperature, time_step_number):
+def scr(input_coor_name, temperature, time_step_number, user_rand):
+    dir_path = 'media/files/' + user_rand + '/'
+    simulation_status_path = dir_path + 'simulation_status.txt'
+    simulation_status_during_run_path = dir_path + 'simulation_status_during_run.txt'
+    trajectory_path = dir_path
     pdb = app.PDBFile(input_coor_name)
     forcefield = app.ForceField('amber99sbildn.xml', 'tip3p.xml')
-
     system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds,
                                      rigidWater=True)
     integrator = mm.LangevinIntegrator(temperature * unit.kelvin, 1.0 / unit.picoseconds, 2.0 * unit.femtoseconds)
     integrator.setConstraintTolerance(0.00001)
 
-    platform = mm.Platform.getPlatformByName('OpenCL')
-    properties = {'OpenCLPrecision': 'mixed'}
-    simulation = app.Simulation(pdb.topology, system, integrator, platform, properties)
+    platform = mm.Platform.getPlatformByName('CPU')
+    
+    simulation = app.Simulation(pdb.topology, system, integrator, platform)
     simulation.context.setPositions(pdb.positions)
 
-    update_simulation_status('Minimizing energy...')
+    update_simulation_status('Minimizing energy...', user_rand)
     simulation.minimizeEnergy()
 
     simulation.context.setVelocitiesToTemperature(temperature * unit.kelvin)
 
-    update_simulation_status('Equilibrating...')
+    update_simulation_status('Equilibrating...', user_rand)
     simulation.step(100)
 
     simulation.reporters.append(app.DCDReporter(trajectory_path + traj_dcd, 1000))
@@ -37,40 +40,46 @@ def scr(input_coor_name, temperature, time_step_number):
         app.StateDataReporter(simulation_status_during_run_path, 1000, progress=True, remainingTime=True,
                               totalSteps=time_step_number, separator=','))
 
-    update_simulation_status('Running simulation...')
+    update_simulation_status('Running simulation...', user_rand)
     simulation.step(time_step_number)
 
 
-def update_simulation_status(status):
+def update_simulation_status(status, user_rand):
+    dir_path = 'media/files/' + user_rand + '/'
+    simulation_status_path = dir_path + 'simulation_status.txt'
+    simulation_status_during_run_path = dir_path + 'simulation_status_during_run.txt'
+    trajectory_path = dir_path
+	
     with open(simulation_status_path, "w+") as f:
         f.write(status)
 
 
-def scr_for_checks(input_coor_name):
-    forcefield = app.ForceField('amber96.xml', 'tip3p.xml')
+def scr_for_checks(input_coor_name, user_rand, full_check=False):
     pdb = app.PDBFile(input_coor_name)
+    forcefield = app.ForceField('amber99sbildn.xml', 'tip3p.xml')
 
-    system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.PME,
-                                     nonbondedCutoff=1.0 * unit.nanometers, constraints=app.HBonds, rigidWater=True,
-                                     ewaldErrorTolerance=0.0005)
-    integrator = mm.LangevinIntegrator(300 * unit.kelvin, 1.0 / unit.picoseconds,
-                                       2.0 * unit.femtoseconds)
-    integrator.setConstraintTolerance(0.00001)
+    # The following line causes an error (when we do not perform "fix pdb")
+    system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds,
+                                     rigidWater=True)
 
-    platform = mm.Platform.getPlatformByName('OpenCL')
-    properties = {'OpenCLPrecision': 'mixed'}
-    simulation = app.Simulation(pdb.topology, system, integrator, platform, properties)
-    simulation.context.setPositions(pdb.positions)
+    if full_check:
+        integrator = mm.LangevinIntegrator(300 * unit.kelvin, 1.0 / unit.picoseconds, 2.0 * unit.femtoseconds)
+        integrator.setConstraintTolerance(0.00001)
 
-    print('Minimizing...')
-    simulation.minimizeEnergy()
+        platform = mm.Platform.getPlatformByName('CPU')
+        
+        simulation = app.Simulation(pdb.topology, system, integrator, platform)
+        simulation.context.setPositions(pdb.positions)
 
-    simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
-    print('Equilibrating...')
-    simulation.step(100)
+        # Minimizing
+        simulation.minimizeEnergy()
+
+        simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)
+
+        # Equilibrating
+        simulation.step(100)
 
-    simulation.reporters.append(app.DCDReporter('media/files/' + 'very_good.dcd', 1000))
+        simulation.reporters.append(app.DCDReporter('media/files/' + user_rand + '/' + 'scr_for_checks.dcd', 1000))
 
-    print('Running Production...')
-    simulation.step(1000)
-    print('Done!')
+        # Running Production
+        simulation.step(1000)
diff --git a/src/SimuMole/SimuMoleScripts/emailSender.py b/src/SimuMole/SimuMoleScripts/emailSender.py
index d0ce66c..240b370 100644
--- a/src/SimuMole/SimuMoleScripts/emailSender.py
+++ b/src/SimuMole/SimuMoleScripts/emailSender.py
@@ -25,8 +25,8 @@
 size_limit = 10 * megabyte
 
 
-def send_email(receiver, file_name):
-    file_name = "./media/files/" + file_name
+def send_email(receiver, file_name, user_rand):
+    file_name = "./media/files/" + user_rand + '/' +  file_name
     size = os.stat(file_name).st_size
     if size < size_limit:
         send_file_attached(receiver, file_name)
diff --git a/src/SimuMole/SimuMoleScripts/simulation_main_script.py b/src/SimuMole/SimuMoleScripts/simulation_main_script.py
index 7193322..50fce4b 100644
--- a/src/SimuMole/SimuMoleScripts/simulation_main_script.py
+++ b/src/SimuMole/SimuMoleScripts/simulation_main_script.py
@@ -1,11 +1,10 @@
 from time import sleep
-import pymol
+import pymol2
+import os
 
 from .fix_pdb import fix_pdb
 from .basicTrajectoryBuilder import scr, update_simulation_status
-from .transformations import translate_pdb
 
-temp = 'media/files/'  # path to temp folder
 pdb = '.pdb'  # pdb suffix
 
 
@@ -13,10 +12,11 @@ class Simulation:
 
     def __init__(self, num_of_proteins, first_pdb_type, first_pdb_id, second_pdb_type, second_pdb_id,
                  x1, y1, z1, x2, y2, z2, degXY_1, degYZ_1, degXY_2, degYZ_2, temperature_scale, temperature,
-                 time_step_number):
+                 time_step_number, user_rand):
 
         self.cmd = None
-
+        self.user_rand = user_rand
+        self.temp =  'media/files/' + self.user_rand + '/'
         self.num_of_proteins = num_of_proteins
 
         self.first_pdb_type = first_pdb_type
@@ -41,104 +41,59 @@ def __init__(self, num_of_proteins, first_pdb_type, first_pdb_id, second_pdb_typ
         self.time_step_number = (int(time_step_number) - 1) * 1000
 
     def create_simulation(self):
-        pymol.finish_launching(['pymol', '-q'])  # pymol: -q quiet launch, -c no gui, -e fullscreen
-        self.cmd = pymol.cmd
-        filename_1 = '_1_'
-        filename_2 = '_2_'
-        if self.num_of_proteins == '2':
-            # STEP 1: load input pdb
-            if self.first_pdb_type == 'by_id':
-                self.save_pdb_by_id(self.first_pdb_id, filename_1 + pdb)
-            if self.second_pdb_type == 'by_id':
-                self.save_pdb_by_id(self.second_pdb_id, filename_2 + pdb)
-
-            # STEP 2: fix positions
-            filename_1_movement = filename_1 + '__movement'
-            filename_2_movement = filename_2 + '__movement'
-            translate_pdb(temp + filename_1 + pdb, temp + filename_1_movement + pdb, self.x1, self.y1, self.z1,
-                          self.degXY_1, self.degYZ_1)
-            translate_pdb(temp + filename_2 + pdb, temp + filename_2_movement + pdb, self.x2, self.y2, self.z2,
-                          self.degXY_2, self.degYZ_2)
-
-            # STEP 2.5: fix pdb
-            fix_pdb(temp + filename_1_movement + pdb)
-            fix_pdb(temp + filename_2_movement + pdb)
-
-            # STEP 3: merge to single pdb file
-            self.save_pdbs_in_one_pdb(filename_1_movement, filename_2_movement)
-
-            # STEP 3.5: fix pdb
-            fix_pdb(temp + "both__" + filename_1_movement + '_' + filename_2_movement + pdb)
-
-            # STEP 4: use OpenMM
-            input_coor_name = temp + "both__" + filename_1_movement + '_' + filename_2_movement + pdb
-            scr(input_coor_name, self.temperature, self.time_step_number)
 
+        #pymol.finish_launching(['pymol', '-q'])  # pymol: -q quiet launch, -c no gui, -e fullscreen
+        #self.cmd = pymol.cmd
+        p1 = pymol2.PyMOL()
+        p1.start()
+        self.cmd = p1.cmd
+
+        # define input files to 'create_simulation_pdb':
+        if self.num_of_proteins == '2':
+            input_coor_name = 'both_1_2'
         else:
-            # STEP 1: load input pdb
-            if self.first_pdb_type == 'by_id':
-                self.save_pdb_by_id(self.first_pdb_id, filename_1 + pdb)
-
-            # STEP 2: fix positions
-            filename_1_movement = filename_1 + '__movement'
-            translate_pdb(temp + filename_1 + pdb, temp + filename_1_movement + pdb, self.x1, self.y1, self.z1,
-                          self.degXY_1, self.degYZ_1)
-
-            # STEP 2.5: fix pdb
-            fix_pdb(temp + filename_1_movement + pdb)
-
-            # STEP 3: use OpenMM
-            input_coor_name = temp + filename_1_movement + pdb
-            try:
-                scr(input_coor_name, self.temperature, self.time_step_number)
-            except:
-                update_simulation_status('An error occurred while creating the simulation. Please try again later.')
-                return
-
-        # save the DCD file using PyMOL
+            input_coor_name = '_1_'
+
         try:
+            # run OpenMM:
+            input_coor_name = self.temp + input_coor_name + pdb
+            fix_pdb(input_coor_name)
+            scr(input_coor_name, self.temperature, self.time_step_number, self.user_rand)
+
+            # save the DCD file using PyMOL
             self.cmd.reinitialize()
+            sleep(0.5)
             self.cmd.load(input_coor_name)
-            self.cmd.load_traj(temp + 'trajectory.dcd')
-        except:  # mainly for "pymol.CmdException"
-            update_simulation_status('An error occurred while creating the simulation. Please try again later.')
+            self.cmd.load_traj(self.temp + 'trajectory.dcd')
+
+        except Exception as e:  # mainly for "pymol.CmdException"
+            print(str(e))
+            update_simulation_status('An error occurred while creating the simulation. Please try again later.', self.user_rand)
             return
 
-        # create the animations:
-        update_simulation_status('Creates the animations')
-        create_movies_from_different_angles(self.cmd)  # create movies in media/movies folder
+        try:
+            # create the animations:
+            update_simulation_status('Creates the animations', self.user_rand)
+            create_movies_from_different_angles(self.cmd, self.user_rand)  # create movies in media/movies folder
+        except Exception as e:  # mainly for "pymol.CmdException"
+            print(str(e))
+            update_simulation_status('An error occurred while creating the animations. Please try again later.', self.user_rand)
+            return
 
         # complete simulation:
-        update_simulation_status('Done!')
-        # self.cmd.quit() # todo: need to close PyMol window
+        update_simulation_status('Done!', self.user_rand)
 
-    def clear_simulation(self):  # todo: complete this! delete all temporary files
+    def clear_simulation(self):  # todo: complete this, need to delete all temporary files
         # os.remove('path/to/files')
         return
 
-    def save_pdb_by_id(self, pdb_id, name_of_file):
-        self.cmd.reinitialize()
-        sleep(0.5)
-
-        self.cmd.load("https://files.rcsb.org/download/" + pdb_id + pdb)
-        self.cmd.zoom()
-        self.cmd.save(temp + name_of_file)
-
-    def save_pdbs_in_one_pdb(self, filename_1, filename_2):
-        self.cmd.reinitialize()
-        sleep(0.5)
-
-        self.cmd.load(temp + filename_1 + pdb)
-        self.cmd.load(temp + filename_2 + pdb)
-        self.cmd.zoom()
-        self.cmd.save(temp + "both__" + filename_1 + '_' + filename_2 + pdb)
-
     @staticmethod
+	#not used
     def merge_pdbs_by_copy(filename_1, filename_2, do_fix=True):
-        merged_pdb = temp + "both__" + filename_1 + "_" + filename_2 + pdb
+        merged_pdb = self.temp + "both__" + filename_1 + "_" + filename_2 + pdb
         merged_file = open(merged_pdb, 'w')
-        file1 = open(temp + filename_1 + pdb)
-        file2 = open(temp + filename_2 + pdb)
+        file1 = open(self.temp + filename_1 + pdb)
+        file2 = open(self.temp + filename_2 + pdb)
         for line in file1:
             if not (line.startswith('MASTER') or line.startswith('END')):
                 merged_file.write(line)
@@ -154,7 +109,8 @@ def merge_pdbs_by_copy(filename_1, filename_2, do_fix=True):
 
 # FUNCTION IS ASSUMING TRAJECTORY AND PDB FILES ARE LOADED
 # output: 3*3 + 1 auto generated movies from different angles
-def create_movies_from_different_angles(cmd):
+def create_movies_from_different_angles(cmd, user_rand):
+    os.mkdir("media/videos/" + user_rand)
     sleep(0.5)
     cmd.do("run SimuMoleScripts/axes.py")
     cmd.do("orient")
@@ -173,7 +129,7 @@ def create_movies_from_different_angles(cmd):
               (0, 0, 90), (0, 0, 180), (0, 0, 270),  # Z axis
               ]
     for x, y, z in angels:
-        update_simulation_status('Creates the animations ({} of {})'.format(i + 1, len(angels)))
+        update_simulation_status('Creates the animations ({} of {})'.format(i + 1, len(angels)), user_rand)
         x, y, z = str(x), str(y), str(z)
         cmd.sync()
         cmd.do("turn x, " + x)
@@ -184,7 +140,7 @@ def create_movies_from_different_angles(cmd):
         cmd.sync()
         cmd.do("zoom complete = 1")
         cmd.sync()
-        cmd.do("movie.produce media/videos/video_" + str(i) + ".mp4, quality = 90,preserve=0")
+        cmd.do("movie.produce media/videos/" + user_rand + "/" + "video_" + str(i) + ".mp4, quality = 90,preserve=0")
         cmd.sync()
         sleep(3)  # Sleep might not be a solution, but without it the commands run too fast and make errors.
         #           Attempting to use the sync command on 'produce' doesnt seem to work.
@@ -194,4 +150,6 @@ def create_movies_from_different_angles(cmd):
         cmd.sync()
         cmd.do("turn x, " + "-" + x)
         cmd.sync()
-        i = i + 1
\ No newline at end of file
+        i = i + 1
+
+    cmd.do("reinitialize")
diff --git a/src/SimuMole/SimuMoleScripts/uploaded_simulation.py b/src/SimuMole/SimuMoleScripts/uploaded_simulation.py
index 383cbb5..b22ba23 100644
--- a/src/SimuMole/SimuMoleScripts/uploaded_simulation.py
+++ b/src/SimuMole/SimuMoleScripts/uploaded_simulation.py
@@ -1,39 +1,44 @@
 import pymol
 from .simulation_main_script import create_movies_from_different_angles
 from .basicTrajectoryBuilder import update_simulation_status
+from time import sleep
 
 temp = 'media/files/'  # path to temp folder
 
 
-def pdb_and_dcd_match(pdb_file_name, dcd_file_name):  # todo: remove gui
+def pdb_and_dcd_match(pdb_file_name, dcd_file_name):
     pymol.finish_launching(['pymol', '-q'])  # pymol: -q quiet launch, -c no gui, -e fullscreen
     cmd = pymol.cmd
     try:
         cmd.reinitialize()
+        sleep(0.5)
         cmd.load(temp + pdb_file_name)
         cmd.load_traj(temp + dcd_file_name)
         return True
-    except:
+    except Exception as e:
+        print(str(e))
         return False
 
 
 def create_animations():
-    # for now, only open pymol window: #todo: create the animations instead of only open PyMOL
-    pymol.finish_launching(['pymol', '-q'])  # pymol: -q quiet launch, -c no gui, -e fullscreen
-    cmd = pymol.cmd
     try:
+        pymol.finish_launching(['pymol', '-q'])  # pymol: -q quiet launch, -c no gui, -e fullscreen
+        cmd = pymol.cmd
+
+        # load input
         cmd.reinitialize()
+        sleep(0.5)
         cmd.load(temp + "file_upload_pdb.pdb")
         cmd.load_traj(temp + "file_upload_dcd.dcd")
-    except:  # mainly for "pymol.CmdException"
-        update_simulation_status(
-            'An error occurred while creating the simulation. Please try again later.')  # todo: change error message!
-        return
 
-    # create the animations:
-    update_simulation_status('Creates the animations')
-    create_movies_from_different_angles(cmd)  # create movies in media/movies folder
+        # create the animations:
+        update_simulation_status('Creates the animations')
+        create_movies_from_different_angles(cmd)  # create movies in media/movies folder
+
+        # complete simulation:
+        update_simulation_status('Done!')
 
-    # complete simulation:
-    update_simulation_status('Done!')
-    # self.cmd.quit() # todo: need to close PyMol window
+    except Exception as e:  # mainly for "pymol.CmdException"
+        print(str(e))
+        update_simulation_status('An error occurred while creating the animations. Please try again later.')
+        return
diff --git a/src/SimuMole/SimuMoleWeb/forms.py b/src/SimuMole/SimuMoleWeb/forms.py
index 90036e0..202cb71 100644
--- a/src/SimuMole/SimuMoleWeb/forms.py
+++ b/src/SimuMole/SimuMoleWeb/forms.py
@@ -7,22 +7,20 @@
 from django.conf import settings
 from SimuMoleScripts.basicTrajectoryBuilder import scr_for_checks
 from SimuMoleScripts.fix_pdb import fix_pdb
-from SimuMoleScripts.transformations import get_atoms, get_atoms_string, translate_vecs, rotate_molecular
+from SimuMoleScripts.transformations import get_atoms, get_atoms_string, translate_vecs, rotate_molecular, translate_pdb
 from SimuMoleScripts.uploaded_simulation import pdb_and_dcd_match
-
+import random
+import string
 import os
+import pymol2
+from time import sleep
 
 ################################
 #   Create Simulation
 ################################
 
-do_checks_cnt = 0
-
 
 class SimulationForm0_LoadPdb(forms.Form):
-    global do_checks
-    do_checks = True
-
     num_of_proteins = forms.ChoiceField(
         required=True,
         label='Choose whether to load one or two proteins',
@@ -46,124 +44,123 @@ class SimulationForm0_LoadPdb(forms.Form):
         widget=forms.RadioSelect)
     second_pdb_id = forms.CharField(required=False, label='Enter your second pdb ID', max_length=10)
     second_pdb_file = forms.FileField(required=False, label='Upload your second pdb file')
-
+    
+    user_rand = forms.CharField(required=False, label='', initial = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(8)))
+    
     @staticmethod
     def save_file(file: UploadedFile, filename: str):
         file_storage = FileSystemStorage(location=os.path.join(settings.MEDIA_ROOT, 'files'))
         file_storage.delete(filename)  # delete existing file with same name (due to clean_my_file previous calls)
         file_storage.save(filename, file)  # save existing file
 
-    @staticmethod
-    def update_cnt():
-        global do_checks_cnt
-        loop_amount = 9
-
-        if do_checks_cnt < loop_amount - 1:
-            do_checks_cnt += 1
-        else:
-            do_checks_cnt = 0
-
     def clean(self):
         cleaned_data = super(SimulationForm0_LoadPdb, self).clean()
-        # data = {**self.initial, **cleaned_data}  # self.initial->from previous steps, cleaned_data->from current step
-        SimulationForm0_LoadPdb.update_cnt()
-        return cleaned_data
-
-    # first pdb validation:
+        data = {**self.initial, **cleaned_data}  # self.initial->from previous steps, cleaned_data->from current step
 
-    def clean_first_pdb_type(self):
-        num_of_proteins = self.cleaned_data['num_of_proteins']
-        first_pdb_type = self.cleaned_data['first_pdb_type']
+        errors = []
+        first_id_exist, first_file_exist, second_id_exist, second_file_exist = False, False, False, False
+
+        # ....................................................................#
+        # check that the form structure is valid
+        # ("field is required" errors)
+        # ....................................................................#
+
+        num_of_proteins = data.get('num_of_proteins', None)
+        first_pdb_type = data.get('first_pdb_type', None)
+        first_pdb_id, first_pdb_file = data.get('first_pdb_id', None), data.get('first_pdb_file', None)
+        second_pdb_type = data.get('second_pdb_type', None)
+        second_pdb_id, second_pdb_file = data.get('second_pdb_id', None), data.get('second_pdb_file', None)
+        user_rand =  data.get('user_rand', None)
+        # clean_first_pdb_type
         if num_of_proteins == '1' or num_of_proteins == '2':
-            if first_pdb_type == '':
-                raise forms.ValidationError("This field is required.")
-        return first_pdb_type
-
-    def clean_first_pdb_id(self):
-        num_of_proteins = self.cleaned_data['num_of_proteins']
-        if self.cleaned_data.get('first_pdb_type') is not None:
-            first_pdb_type = self.cleaned_data['first_pdb_type']
-            first_pdb_id = self.cleaned_data['first_pdb_id']
+            if (first_pdb_type is None) or (first_pdb_type == ''):
+                errors.append(forms.ValidationError("First protein: The 'PDB type' field is required."))
+
+        # clean_first_pdb_id
+        if first_pdb_type is not None:
             if (num_of_proteins == '1' or num_of_proteins == '2') and first_pdb_type == 'by_id':
-                if first_pdb_id == '':
-                    raise forms.ValidationError("This field is required.")
+                if (first_pdb_id is None) or (first_pdb_id == ''):
+                    errors.append(forms.ValidationError("First protein: The 'by id' field is required."))
                 else:
-                    self.pdb_id_validation(first_pdb_id)
-            return first_pdb_id
+                    first_id_exist = True
 
-    def clean_first_pdb_file(self):
-        num_of_proteins = self.cleaned_data['num_of_proteins']
-        if self.cleaned_data.get('first_pdb_type') is not None:
-            first_pdb_type = self.cleaned_data['first_pdb_type']
+        # clean_first_pdb_file
+        if first_pdb_type is not None:
             first_pdb_file: UploadedFile = self.cleaned_data['first_pdb_file']
             if (num_of_proteins == '1' or num_of_proteins == '2') and first_pdb_type == 'by_file':
-                if first_pdb_file == '':
-                    raise forms.ValidationError("This field is required.")
+                if (first_pdb_file is None) or (first_pdb_file == ''):
+                    errors.append(forms.ValidationError("First protein: The 'by file' field is required."))
                 else:
-                    pass
-                    # self.pdb_file_validation(first_pdb_file)
-                    # TODO: fix
-                self.save_file(first_pdb_file, "_1_.pdb")
-            return first_pdb_file
+                    first_file_exist = True
 
-    # second pdb validation:
-
-    def clean_second_pdb_type(self):
-        num_of_proteins = self.cleaned_data['num_of_proteins']
-        second_pdb_type = self.cleaned_data['second_pdb_type']
+        # clean_second_pdb_type
         if num_of_proteins == '2':
-            if second_pdb_type == '':
-                raise forms.ValidationError("This field is required.")
-        return second_pdb_type
-
-    def clean_second_pdb_id(self):
-        num_of_proteins = self.cleaned_data['num_of_proteins']
-        if self.cleaned_data.get('second_pdb_type') is not None:
-            second_pdb_type = self.cleaned_data['second_pdb_type']
-            second_pdb_id = self.cleaned_data['second_pdb_id']
+            if (second_pdb_type is None) or (second_pdb_type == ''):
+                errors.append(forms.ValidationError("Second protein: The 'PDB type' field is required."))
+
+        # clean_second_pdb_id
+        if second_pdb_type is not None:
             if (num_of_proteins == '2') and second_pdb_type == 'by_id':
-                if second_pdb_id == '':
-                    raise forms.ValidationError("This field is required.")
+                if (second_pdb_id is None) or (second_pdb_id == ''):
+                    errors.append(forms.ValidationError("Second protein: The 'by id' field is required."))
                 else:
-                    self.pdb_id_validation(second_pdb_id)
-            return second_pdb_id
+                    second_id_exist = True
 
-    def clean_second_pdb_file(self):
-        num_of_proteins = self.cleaned_data['num_of_proteins']
-        if self.cleaned_data.get('second_pdb_type') is not None:
-            second_pdb_type = self.cleaned_data['second_pdb_type']
+        # clean_second_pdb_file
+        if second_pdb_type is not None:
             second_pdb_file: UploadedFile = self.cleaned_data['second_pdb_file']
             if (num_of_proteins == '2') and second_pdb_type == 'by_file':
-                if second_pdb_file == '':
-                    raise forms.ValidationError("This field is required.")
+                if (second_pdb_file is None) or (second_pdb_file == ''):
+                    errors.append(forms.ValidationError("Second protein: The 'by file' field is required."))
                 else:
-                    pass
-                    # self.pdb_file_validation(second_pdb_file)
-                    # TODO: fix
-                self.save_file(second_pdb_file, "_2_.pdb")
-            return second_pdb_file
+                    second_file_exist = True
 
-    # pdb validation checks:
-
-    def pdb_id_validation(self, pdb_id):
-        global do_checks_cnt
-        if do_checks_cnt != 0:
-            return
+        if len(errors) != 0:
+            raise forms.ValidationError(errors)
 
-        if not self.pdb_id_exists(pdb_id):
-            raise forms.ValidationError("invalid PDB id")
+        # ....................................................................#
+        # check that the input PDBs structure is valid
+        # ("Invalid PDB id" / "Protein not supported by OpenMM" errors)
+        # ....................................................................#
+        if (not os.path.exists("media/files/" + user_rand)):
+            os.mkdir("media/files/" + user_rand)
+        
+        if first_id_exist:
+            pdb_validation_result = self.pdb_id_validation(first_pdb_id, "_1_.pdb", user_rand)
+            if pdb_validation_result is not None:
+                errors.append(forms.ValidationError("First protein: " + pdb_validation_result))
+        if first_file_exist:
+            self.save_file(first_pdb_file, "_1_.pdb")
+            pdb_validation_result = self.pdb_file_validation("media/files/" + user_rand + '/' + "_1_.pdb", user_rand)
+            if pdb_validation_result is not None:
+                errors.append(forms.ValidationError("First protein: " + pdb_validation_result))
+        if second_id_exist:
+            pdb_validation_result = self.pdb_id_validation(second_pdb_id, "_2_.pdb", user_rand)
+            if pdb_validation_result is not None:
+                errors.append(forms.ValidationError("Second protein: " + pdb_validation_result))
+        if second_file_exist:
+            self.save_file(second_pdb_file, "_2_.pdb")
+            pdb_validation_result = self.pdb_file_validation("media/files/"  + user_rand + '/' +  "_2_.pdb", user_rand)
+            if pdb_validation_result is not None:
+                errors.append(forms.ValidationError("Second protein: " + pdb_validation_result))
 
-        # if not self.pdb_id_valid(pdb_id):
-        #     raise forms.ValidationError("Protein not supported by OpenMM")
-        # TODO: fix
+        if len(errors) != 0:
+            raise forms.ValidationError(errors)
+        
+        #cleaned_data['user_rand'] = user_rand
+        return cleaned_data
 
-    def pdb_file_validation(self, pdb_id):
-        global do_checks_cnt
-        if do_checks_cnt != 0:
-            return
+    def pdb_id_validation(self, pdb_id, filename, user_rand):
+        if not self.pdb_id_exists(pdb_id):
+            return "Invalid PDB id"
+        if not self.pdb_id_valid(pdb_id, filename, user_rand):
+            return "Protein not supported by OpenMM"
+        return None
 
-        if not self.pdb_file_valid(pdb_id):
-            raise forms.ValidationError("Protein not supported by OpenMM")
+    def pdb_file_validation(self, pdb_id, user_rand):
+        if not self.pdb_file_valid(pdb_id, user_rand):
+            return "Protein not supported by OpenMM"
+        return None
 
     @staticmethod
     def pdb_id_exists(pdb_id):
@@ -173,39 +170,39 @@ def pdb_id_exists(pdb_id):
         return True
 
     @staticmethod
-    def download_pdb(pdb_id):
+    def download_pdb(pdb_id, filename, user_rand):
         response = requests.get("https://files.rcsb.org/view/" + pdb_id + ".pdb")
-        pdb_file_name = "media/files/" + pdb_id + ".pdb"
+        pdb_file_name = "media/files/" + user_rand + '/' + filename
         pdb_file = open(pdb_file_name, 'w')
         pdb_file.write(response.text)
         pdb_file.close()
         response.close()
         return pdb_file_name
 
-    '''
-    Checks whether a pdb id can be used in an openMM simulation by downloading the relevant file and testing it.
-    This function assumes the id is valid.
-    '''
-
     @staticmethod
-    def pdb_id_valid(pdb_id):
-        pdb_file_name = SimulationForm0_LoadPdb.download_pdb(pdb_id)
-        return SimulationForm0_LoadPdb.pdb_file_valid(pdb_file_name)
-
-    '''
-    Checks if the given file can be used in an openMM simulation.
-    If it can run without fixing then it returns true.
-    If it can run with fixing it will return true AND fix the file.
-    Otherwise it returns false.
-    '''
+    def pdb_id_valid(pdb_id, filename, user_rand):
+        """
+        Checks whether a pdb id can be used in an openMM simulation by downloading the relevant file and testing it.
+        This function assumes the id is valid.
+        """
+        pdb_file_name = SimulationForm0_LoadPdb.download_pdb(pdb_id, filename, user_rand)
+        return SimulationForm0_LoadPdb.pdb_file_valid(pdb_file_name, user_rand)
 
     @staticmethod
-    def pdb_file_valid(pdb_file):
-        dcd_file = "media/files/very_good.dcd"
+    def pdb_file_valid(pdb_file_name, user_rand):
+        """
+        Checks if the given file can be used in an openMM simulation.
+        If it can run without fixing then it returns true.
+        If it can run with fixing it will return true AND fix the file.
+        Otherwise it returns false.
+        """
+        dcd_file = "media/files/" + user_rand + '/' + "scr_for_checks.dcd"
+
         fix_not_needed = True
         try:
-            scr_for_checks(pdb_file)
-        except Exception:
+            scr_for_checks(pdb_file_name, user_rand)
+        except Exception as e:
+            # print(str(e))
             fix_not_needed = False
         finally:
             if os.path.exists(dcd_file):
@@ -215,13 +212,12 @@ def pdb_file_valid(pdb_file):
             return True
 
         try:
-            fix_pdb(pdb_file)
-            scr_for_checks(pdb_file)
-        except Exception:
+            fix_pdb(pdb_file_name)
+            scr_for_checks(pdb_file_name, user_rand)
+        except Exception as e:
+            print(str(e))
             return False
-        finally:
-            if os.path.exists(dcd_file):
-                os.remove(dcd_file)
+
         return True
 
 
@@ -245,20 +241,48 @@ def clean(self):
             if data[field] == '' or data[field] is None:
                 raise forms.ValidationError("All fields are required.")
 
-        if not self.position_is_valid(data['x1'], data['y1'], data['z1'],
-                                      data['x2'], data['y2'], data['z2'],
-                                      data['degXY_1'], data['degYZ_1'], data['degXY_2'], data['degYZ_2'],
-                                      data['first_pdb_id'], data['second_pdb_id'], data['first_pdb_type'],
-                                      data['second_pdb_type'], data['first_pdb_file'], data['second_pdb_file']):
+        if not self.position_is_valid(data['x1'], data['y1'], data['z1'], data['x2'], data['y2'], data['z2'],
+                                      data['degXY_1'], data['degYZ_1'], data['degXY_2'], data['degYZ_2'], data['user_rand']):
             raise forms.ValidationError("Positions are not possible: The proteins collide with each other")
 
+        self.change_relative_position(data['x1'], data['y1'], data['z1'], data['x2'], data['y2'], data['z2'],
+                                      data['degXY_1'], data['degYZ_1'], data['degXY_2'], data['degYZ_2'], data['user_rand'])
+
         return cleaned_data
 
     @staticmethod
-    def position_is_valid(x1, y1, z1, x2, y2, z2, degXY_1, degYZ_1, degXY_2, degYZ_2,
-                          first_pdb_id, second_pdb_id, first_pdb_type, second_pdb_type,
-                          first_pdb_file, second_pdb_file):
-        # DONE 6: check with PyMol that the proteins do not collide with each other (need to add the pdbs parameters)
+    def change_relative_position(x1, y1, z1, x2, y2, z2, degXY_1, degYZ_1, degXY_2, degYZ_2, user_rand):
+        """
+        Save PDB file that represents the 2 PDB files after you change the positions and running pdb_fixer
+        """
+        # change positions
+        filename_1, filename_2, pdb, temp = '_1_', '_2_', '.pdb', 'media/files/' + user_rand + '/'
+        filename_1_movement, filename_2_movement = filename_1 + '__movement', filename_2 + '__movement'
+        translate_pdb(temp + filename_1 + pdb, temp + filename_1_movement + pdb, x1, y1, z1, degXY_1, degYZ_1)
+        translate_pdb(temp + filename_2 + pdb, temp + filename_2_movement + pdb, x2, y2, z2, degXY_2, degYZ_2)
+
+        # fix pdb
+        fix_pdb(temp + filename_1_movement + pdb)
+        fix_pdb(temp + filename_2_movement + pdb)
+
+        # merge to single pdb file
+        #pymol.finish_launching(['pymol', '-q'])  # pymol: -q quiet launch, -c no gui, -e fullscreen
+        #cmd = pymol.cmd
+        p1 = pymol2.PyMOL()
+        p1.start()
+        cmd = p1.cmd
+        cmd.reinitialize()
+        sleep(0.5)
+        cmd.load(temp + filename_1_movement + pdb)
+        cmd.load(temp + filename_2_movement + pdb)
+        cmd.zoom()
+        cmd.save(temp + "both_1_2" + pdb)
+
+    @staticmethod
+    def position_is_valid(x1, y1, z1, x2, y2, z2, degXY_1, degYZ_1, degXY_2, degYZ_2, user_rand):
+        """
+        check with PyMol that the proteins do not collide with each other
+        """
 
         # return max X,Y,Z locations from all the atoms in vecs
         def get_max_XYZ(vecs):
@@ -269,18 +293,12 @@ def get_min_XYZ(vecs):
             return min(vecs, key=lambda v: v[0])[0], min(vecs, key=lambda v: v[1])[1], min(vecs, key=lambda v: v[2])[2]
 
         # get the atoms of the first protein after moving it in x1,y1,z1
-        if first_pdb_type == 'by_id':
-            vecs1 = get_atoms_string(requests.get('https://files.rcsb.org/view/' + first_pdb_id + '.pdb').text)
-        else:
-            vecs1 = get_atoms('media/files/_1_.pdb')
+        vecs1 = get_atoms('media/files/' + user_rand + '/' + '_1_.pdb')
         translate_vecs(x1, y1, z1, vecs1)
         rotate_molecular(x1, y1, z1, degXY_1, degYZ_1, vecs1)
 
         # get the atoms of the second protein after moving it in x2,y2,z2
-        if second_pdb_type == 'by_id':
-            vecs2 = get_atoms_string(requests.get("https://files.rcsb.org/view/" + second_pdb_id + ".pdb").text)
-        else:
-            vecs2 = get_atoms('media/files/_2_.pdb')
+        vecs2 = get_atoms('media/files/' + user_rand + '/' + '_2_.pdb')
         translate_vecs(x2, y2, z2, vecs2)
         rotate_molecular(x2, y2, z2, degXY_2, degYZ_2, vecs2)
 
@@ -311,9 +329,6 @@ class SimulationForm2_SimulationParameters(forms.Form):
         widget=forms.RadioSelect, initial='celsius')
     temperature = forms.FloatField(required=False, label='Enter temperature', initial=30)
 
-    # time_step_duration = forms.FloatField(required=False,
-    #                                       label='Enter the duration of the time step (in fs/femto-second)',
-    #                                       initial=2.0) // todo: check if we can add this field
     time_step_number = forms.IntegerField(required=False, label='Enter the number of time steps (frames)', initial=5)
 
     def clean(self):
diff --git a/src/SimuMole/SimuMoleWeb/templates/create_simulation.html b/src/SimuMole/SimuMoleWeb/templates/create_simulation.html
index 548557b..a2945cd 100644
--- a/src/SimuMole/SimuMoleWeb/templates/create_simulation.html
+++ b/src/SimuMole/SimuMoleWeb/templates/create_simulation.html
@@ -127,7 +127,15 @@ <h3>Set the parameters for the simulation</h3>
         <!-- loading spinner -->
         <div id="loading_spinner">
             <div class="spinner" id="spinner-image"></div>
-            <div id="spinner-text"><p>Loading...</p></div>
+            <div id="spinner-text">
+                {% if  wizard.steps.current  == '0' %}
+                    <p>Checks that the PDB is valid (ID exist / file format is correct), and supported by OpenMM</p>
+                {% elif  wizard.steps.current == '1' %}
+                    <p>Checks that the position is legal (the proteins do not collide with each other)</p>
+                {% elif  wizard.steps.current == '2' %}
+                    <p>Validates your request</p>
+                {% endif %}
+            </div>
         </div>
 
     </form>
@@ -289,7 +297,7 @@ <h3>Set the parameters for the simulation</h3>
         function hide_errorlist() {
             let errors = document.getElementsByClassName("errorlist");
             for (let l = 0; l < errors.length; l++) {
-                errors[l].style.display = 'none';
+                {#errors[l].style.display = 'none';#}
             }
         }
 
diff --git a/src/SimuMole/SimuMoleWeb/templates/create_simulation_result.html b/src/SimuMole/SimuMoleWeb/templates/create_simulation_result.html
index 7663dfa..18c7df8 100644
--- a/src/SimuMole/SimuMoleWeb/templates/create_simulation_result.html
+++ b/src/SimuMole/SimuMoleWeb/templates/create_simulation_result.html
@@ -348,6 +348,9 @@ <h3>Download output files</h3>
             $.ajax({
                 url: '{% url 'update_simulation_status' %}',
                 type: "get",
+				data: {
+                    'user_rand': "{{user_rand}}",
+                },
                 dataType: 'json',
                 success: function (data) {
 
@@ -425,6 +428,7 @@ <h3>Download output files</h3>
                     'dcd_file': dcd_file,
                     'animation_files': animations_files,
                     'previous_page': "{{ previous_page }}",
+					'user_rand': "{{user_rand}}",
                 },
                 dataType: 'json',
                 success: function () {
@@ -459,6 +463,7 @@ <h3>Download output files</h3>
                     'animation_files': animations_files,
                     'email': email,
                     'previous_page': "{{ previous_page }}",
+					'user_rand': "{{user_rand}}",
                 },
                 dataType: 'json',
                 success:
diff --git a/src/SimuMole/SimuMoleWeb/templates/home.html b/src/SimuMole/SimuMoleWeb/templates/home.html
index 463653b..1ff056a 100644
--- a/src/SimuMole/SimuMoleWeb/templates/home.html
+++ b/src/SimuMole/SimuMoleWeb/templates/home.html
@@ -71,7 +71,7 @@ <h3>Technologies</h3>
                 <td>
                     <p style="font-size: large">
                         <strong>PyMOL:</strong> a user-sponsored molecular visualization </p>
-                    <p>Used for displaying the simulations.</p> {# todo: chnage this #}
+                    <p>Used for displaying the simulations.</p>
                 </td>
             </tr>
             <tr>
diff --git a/src/SimuMole/SimuMoleWeb/views.py b/src/SimuMole/SimuMoleWeb/views.py
index 33fd84c..2114128 100644
--- a/src/SimuMole/SimuMoleWeb/views.py
+++ b/src/SimuMole/SimuMoleWeb/views.py
@@ -25,43 +25,29 @@ def home(request):
     return render(request, 'home.html', some_dict)
 
 
-def news(request):
-    some_dict = {}
-    return render(request, 'news.html', some_dict)
-
-
-def contact(request):
-    some_dict = {}
-    return render(request, 'contact.html', some_dict)
-
-
-def about(request):
-    some_dict = {}
-    return render(request, 'about.html', some_dict)
-
-
 ################################
 #   Simulation Result
 ################################
 
 def update_simulation_status(request):
-    f = open(os.path.join(settings.MEDIA_ROOT, 'files', 'simulation_status.txt'), 'r')
+    user_rand = request.GET.get('user_rand')
+    f = open(os.path.join(settings.MEDIA_ROOT, 'files' ,user_rand , 'simulation_status.txt'), 'r')
     simulation_status = f.read()
     f.close()
 
-    f = open(os.path.join(settings.MEDIA_ROOT, 'files', 'simulation_status_during_run.txt'), 'r')
+    f = open(os.path.join(settings.MEDIA_ROOT, 'files',user_rand, 'simulation_status_during_run.txt'), 'r')
     simulation_status_during_run_lines = f.readlines()
     simulation_status_during_run = '' if len(simulation_status_during_run_lines) == 0 \
         else simulation_status_during_run_lines[-1]
     f.close()
 
-    video_url = settings.MEDIA_URL + 'videos/'
+    video_url = settings.MEDIA_URL + 'videos/' + user_rand + '/'
     context = {'simulation_status': simulation_status, 'simulation_status_during_run': simulation_status_during_run,
                'video_path': video_url}
     return JsonResponse(context)
 
 
-def download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, include_animations_files, previous_page):
+def download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, include_animations_files, previous_page, user_rand):
     files = []
     files_names = []
 
@@ -69,19 +55,19 @@ def download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, in
         if previous_page == 'create_simulation':
             file_name = ''
             if num_of_proteins == '1':
-                file_name = '_1___movement.pdb'
+                file_name = '_1_.pdb'
             if num_of_proteins == '2':
-                file_name = 'both___1___movement__2___movement.pdb'
-            files.append(os.path.join(settings.MEDIA_ROOT, 'files', file_name))
+                file_name = 'both_1_2.pdb'
+            files.append(os.path.join(settings.MEDIA_ROOT, 'files', user_rand, file_name))
         if previous_page == 'upload_files':
-            files.append(os.path.join(settings.MEDIA_ROOT, 'files', 'file_upload_pdb.pdb'))
+            files.append(os.path.join(settings.MEDIA_ROOT, 'files', user_rand, 'file_upload_pdb.pdb'))
         files_names.append('pdb.pdb')
 
     if include_dcd_file:
         if previous_page == 'create_simulation':
-            files.append(os.path.join(settings.MEDIA_ROOT, 'files', 'trajectory.dcd'))
+            files.append(os.path.join(settings.MEDIA_ROOT, 'files',user_rand, 'trajectory.dcd'))
         if previous_page == 'upload_files':
-            files.append(os.path.join(settings.MEDIA_ROOT, 'files', 'file_upload_dcd.dcd'))
+            files.append(os.path.join(settings.MEDIA_ROOT, 'files',user_rand, 'file_upload_dcd.dcd'))
         files_names.append('dcd.dcd')
 
     if include_animations_files:
@@ -91,30 +77,31 @@ def download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, in
                   (0, 0, 90), (0, 0, 180), (0, 0, 270), ]  # Z axis
         for i, (x, y, z) in zip(range(0, 10), angels):
             video_name = 'video_{}.mp4'.format(str(i))
-            files.append(os.path.join(settings.MEDIA_ROOT, 'videos', video_name))
+            files.append(os.path.join(settings.MEDIA_ROOT, 'videos', user_rand, video_name))
             video_name_at_download = 'video_{}__X{}_Y{}_Z{}.mp4'.format(str(i), str(x), str(y), str(z))
             files_names.append(video_name_at_download)
 
-    print(files_names)
-    zip_file = zipfile.ZipFile(os.path.join(settings.MEDIA_ROOT, 'files', "SimuMole_output.zip"), "w")
+    zip_file = zipfile.ZipFile(os.path.join(settings.MEDIA_ROOT, 'files',user_rand, "SimuMole_output.zip"), "w")
     for file, file_name in zip(files, files_names):
         zip_file.write(file, file_name)
     zip_file.close()
 
 
 def download__zip(request):
+    user_rand = request.GET.get('user_rand')
     num_of_proteins = request.GET.get('num_of_proteins')
     include_pdb_file = (request.GET.get('pdb_file') == 'true')
     include_dcd_file = (request.GET.get('dcd_file') == 'true')
     include_animations_files = (request.GET.get('animation_files') == 'true')
     previous_page = request.GET.get('previous_page')
 
-    download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, include_animations_files, previous_page)
+    download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, include_animations_files, previous_page, user_rand)
 
     return JsonResponse({})
 
 
 def download__email(request):
+    user_rand = request.GET.get('user_rand')
     num_of_proteins = request.GET.get('num_of_proteins')
     include_pdb_file = (request.GET.get('pdb_file') == 'true')
     include_dcd_file = (request.GET.get('dcd_file') == 'true')
@@ -126,8 +113,8 @@ def download__email(request):
     response = {'email_success': 'true'}
     try:
         download__create_zip(num_of_proteins, include_pdb_file, include_dcd_file, include_animations_files,
-                             previous_page)
-        send_email(email, "SimuMole_output.zip")
+                             previous_page, user_rand)
+        send_email(email, "SimuMole_output.zip", user_rand)
     except Exception:
         response = {'email_success': 'false'}
 
@@ -161,7 +148,7 @@ def clean_form_dict(self, dict_):
         degXY_1, degYZ_1, degXY_2, degYZ_2 = '0', '0', '0', '0'
 
         num_of_proteins = dict_.get('num_of_proteins')
-
+        user_rand = dict_.get('user_rand')
         first_pdb_type = dict_.get('first_pdb_type')
         if first_pdb_type == 'by_id':
             first_pdb_id = dict_.get('first_pdb_id')
@@ -187,7 +174,8 @@ def clean_form_dict(self, dict_):
         temperature_scale = dict_.get('temperature_scale', '')
         temperature = dict_.get('temperature', '')
         time_step_number = dict_.get('time_step_number', '')
-
+		
+        clean_dict['user_rand'] = user_rand
         clean_dict['num_of_proteins'] = num_of_proteins
         clean_dict['first_pdb_type'] = first_pdb_type
         clean_dict['first_pdb_id'] = first_pdb_id
@@ -220,7 +208,7 @@ def create_simulation_thread(self, form_dict):
                        form_dict['degXY_1'], form_dict['degYZ_1'],
                        form_dict['degXY_2'], form_dict['degYZ_2'],
                        form_dict['temperature_scale'], form_dict['temperature'],
-                       form_dict['time_step_number'])
+                       form_dict['time_step_number'], form_dict['user_rand'])
         s.create_simulation()
 
     def done(self, form_list, **kwargs):
@@ -238,16 +226,16 @@ def done(self, form_list, **kwargs):
         t.start()
 
         # Initialize the status file:
-        with open(os.path.join(settings.MEDIA_ROOT, 'files', 'simulation_status.txt'), "w+") as f:
+        with open(os.path.join(settings.MEDIA_ROOT, 'files' , form_dict['user_rand'] , 'simulation_status.txt'), "w+") as f:
             f.write("Processing your parameters...")
-        with open(os.path.join(settings.MEDIA_ROOT, 'files', 'simulation_status_during_run.txt'), "w+") as f:
+        with open(os.path.join(settings.MEDIA_ROOT, 'files', form_dict['user_rand'], 'simulation_status_during_run.txt'), "w+") as f:
             f.write("")
 
         # Render 'create_simulation_result.html' without waiting until the simulation is complete:
         return render(self.request, 'create_simulation_result.html',
                       {'form_data': form_dict, 'num_of_proteins': form_dict['num_of_proteins'],
                        'previous_page': 'create_simulation',
-                       'video_path': settings.MEDIA_URL + 'videos/'})  # todo: change "video_path"
+                       'video_path': settings.MEDIA_URL + 'videos/' + form_dict['user_rand'] + '/', 'user_rand':form_dict['user_rand']})
 
     def get_form_initial(self, step):
         """
@@ -264,8 +252,8 @@ def get_form_initial(self, step):
                   'first_pdb_file': step_0_prev_data.get('0-first_pdb_file'),
                   'second_pdb_type': step_0_prev_data.get('0-second_pdb_type'),
                   'second_pdb_id': step_0_prev_data.get('0-second_pdb_id'),
-                  'second_pdb_file': step_0_prev_data.get('0-second_pdb_file'), }
-
+                  'second_pdb_file': step_0_prev_data.get('0-second_pdb_file'), 
+				  'user_rand': step_0_prev_data.get('0-user_rand'),}
         # SimulationForm1_DetermineRelativePosition
         step_1_prev_data = self.storage.get_step_data('1')
         step_1_prev_data = {} if step_1_prev_data is None \
@@ -291,7 +279,7 @@ def show_form1(wizard: CookieWizardView):
     if 'num_of_proteins'==1: return FALSE, and then navigate to step 2 (simulation parameters)
     else, if 'num_of_proteins'==2: return TRUE, and then navigate to step 1 (determine relative position)
     """
-    cleaned_data = wizard.get_cleaned_data_for_step('0') or {}
+    cleaned_data = wizard.get_form_initial('0') or {}
     return cleaned_data.get('num_of_proteins') == '2'
 
 
@@ -315,9 +303,9 @@ def upload_files(request):
                 f.write("")
 
             return render(request, 'create_simulation_result.html',
-                          {'video_path': settings.MEDIA_URL + 'videos/',  # todo: change "video_path"
+                          {'video_path': settings.MEDIA_URL + 'videos/',
                            'previous_page': "upload_files",
                            'num_of_proteins': 0})  # num_of_proteins is irrelevant
     else:
         form = UploadFiles()
-    return render(request, 'file_upload.html', {'form': form})
\ No newline at end of file
+    return render(request, 'file_upload.html', {'form': form})
diff --git a/src/SimuMole/media/files/_init_folder_file.txt b/src/SimuMole/media/files/_init_folder_file.txt
deleted file mode 100644
index e73b925..0000000
--- a/src/SimuMole/media/files/_init_folder_file.txt
+++ /dev/null
@@ -1 +0,0 @@
-This file is intended to initialize the "files" folder (git does not upload empty folders)
\ No newline at end of file