From eb3b14ef3b80b49324f86de06ec0f4cb67ac53ad Mon Sep 17 00:00:00 2001
From: Wes Foyd <wesfloyd@gmail.com>
Date: Fri, 29 Jul 2022 15:00:32 +0000
Subject: [PATCH] updating input file location

---
 Dockerfile               |  2 +-
 README.md                | 12 ++++++------
 run_openmm_simulation.py |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ccb3b8d..ce7ac97 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,6 +5,6 @@ RUN conda install -y -c conda-forge openmm
 WORKDIR /project
 
 COPY ./run_openmm_simulation.py /project
-COPY ./input/2dri-processed.pdb /project/input
+COPY ./2dri-processed.pdb /project
 
 CMD ["python","run_openmm_simulation.py"]
\ No newline at end of file
diff --git a/README.md b/README.md
index 8fc5e4b..57c5cec 100644
--- a/README.md
+++ b/README.md
@@ -28,6 +28,8 @@ bacalhau get [JOB_ID]
 
 #git clone https://github.com/wesfloyd/openmm-test.git
 
+mkdir output
+
 docker run \
 	-v output:/project/output \
 	wesfloyd/bacalwow-openmm
@@ -36,15 +38,13 @@ docker run \
 ```
 
 
-
-
-
 ### To create the Docker image from Dockerfile
-
+```bash
 docker build -t wesfloyd/bacalwow-openmm .
 
 docker push wesfloyd/bacalwow-openmm
 
+```
 
 ### To create the Docker Image from scratch
 
@@ -67,8 +67,8 @@ cp openmm-test/input/2dri-processed.pdb ./input
 python run_openmm_simulation.py
 
 #exit
-#docker commit <CONTAINER_ID> wesfloyd/bacalwow-openmm-test
-#docker push wesfloyd/bacalwow-openmm-test
+#docker commit <CONTAINER_ID> wesfloyd/bacalwow-openmm
+#docker push wesfloyd/bacalwow-openmm
 
 ```
 
diff --git a/run_openmm_simulation.py b/run_openmm_simulation.py
index 14557e4..1ee6885 100644
--- a/run_openmm_simulation.py
+++ b/run_openmm_simulation.py
@@ -6,7 +6,7 @@
 
 # Input Files
 
-pdb = PDBFile('input/2dri-processed.pdb')
+pdb = PDBFile('2dri-processed.pdb')
 forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
 
 # System Configuration