Feature/nwchem

bin/run.sh

@@ -6,6 +6,22 @@ which radical-stack
 hostname
 
 radical-stack
+
+# HDF5 often fails to lock files on compute nodes
+# so best turn locking off to prevent failures
+# in the reporter.
+#
+# The error message in question is:
+# "Unable to create file (unable to lock file, errno = 524, error message = 'Unknown error 524')"
+#
+# More information on this error:
+# https://github.com/nanoporetech/medaka/issues/240
+#
+# See for the reporter h5py code: 
+# - MD-tools/mdtools/openmm/reporter.py
+# - MD-tools/mdtools/nwchem/reporter.py
+export HDF5_USE_FILE_LOCKING="FALSE"
 
-python  -m deepdrivemd.deepdrivemd_stream -c bba/$1/config.yaml
+#python  -m deepdrivemd.deepdrivemd_stream -c bba/$1/config.yaml
+python  -m deepdrivemd.deepdrivemd -c $1/config.yaml
 

data/7cz4/README.md

@@ -0,0 +1,19 @@
+# 7CZ4 - NSP3 macro domain with bound ligand
+
+The structures stored in this directory relate to the ligand binding use case.
+The original structure was obtained from the protein databank ID
+[7CZ4](https://www.rcsb.org/structure/7cz4).
+The initial structure was incomplete missing some heavy atoms as well 
+as Hydrogens. This structure was "fixed" with 
+[Moprobity](http://molprobity.biochem.duke.edu/) and
+[PDBFixer](https://github.com/openmm/pdbfixer). 
+Finally, only the monomer of the protein was kept. The resulting structure
+is stored in `7CZ4-folded.pdb`. This name is analogous to the way systems 
+are named in the `bba` directory. 
+More details on how this structure was prepared can be found at
+<https://github.com/hjjvandam/nwchem-1/tree/pretauadio2/QA/tests/7cz4>.
+
+The structure in `system/7CZ4-unfolded.pdb` was created by first shifting
+the ligand out of the protein, and subsequently running dynamics on it at 
+310K. Conventional dynamics was not able to have the ligand find its binding
+location.