Hack in relative paths.

run_pretrained-Espaloma-0.3.0/run_pretrained.py

@@ -1,4 +1,9 @@
+
+# Hello! Many thanks for the reply. I'm trying to build a box of small molecules only. So I've allowed the topology to be the same as my 'molecule'. If there is only one molecule it works (sure) but if it's >1 the problem remains. My .py now looks something like this. My workflow begins with packmol'ing two small molecules and that is the Y6_2_out.mol/.gro
+
 import os
+pwd=os.getcwd()
+
 import torch
 import espaloma as esp
 
@@ -14,8 +19,8 @@
 from openff.toolkit.utils.toolkits import RDKitToolkitWrapper
 
 # read in molecules to molecular dynamics
-startpositions = GromacsGroFile('/home/hy2120/single-y6/Y6ethyls_pbe0-pvtz.gro').positions
-mol_filepath = get_data_file_path('/home/hy2120/single-y6/Y6ethyls_pbe0-pvtz.mol') 
+startpositions = GromacsGroFile(pwd+'/single-y6/espaloma_on_single_y6/dimer/Y6_2_out.gro').positions
+mol_filepath = get_data_file_path(pwd+'/single-y6/espaloma_on_single_y6/dimer/Y6_2_out.mol') 
 
 # See here: https://docs.openforcefield.org/projects/toolkit/en/stable/users/molecule_cookbook.html#from-small-molecule-pdb-file
 molecule = Molecule.from_file(mol_filepath,"mol", toolkit_registry=RDKitToolkitWrapper())
@@ -40,3 +45,4 @@
 simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
         potentialEnergy=True, temperature=True))
 simulation.step(10000)
+