updating input file location

wesfloyd · Jul 29, 2022 · eb3b14e · eb3b14e
1 parent f4dfb8c
commit eb3b14e
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git 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"]
diff --git 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
@@ -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