From 64e2116d65819c31f2eae8686744f2130e2e6ac1 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 6 Feb 2026 08:17:38 -0800 Subject: [PATCH] comment out md simulation exectution so it doesn't auto-run in testing --- openmm_md/plain_md.ipynb | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/openmm_md/plain_md.ipynb b/openmm_md/plain_md.ipynb index 5c7af2d..bd99f88 100644 --- a/openmm_md/plain_md.ipynb +++ b/openmm_md/plain_md.ipynb @@ -462,13 +462,14 @@ "dag = protocol.create(stateA=system, stateB=system, mapping=None)\n", "workdir = pathlib.Path('./')\n", "# Running the MD simulations\n", - "dagres = gufe.protocols.execute_DAG(\n", - " dag,\n", - " shared_basedir=workdir,\n", - " scratch_basedir=workdir,\n", - " keep_shared=True, # set this to True to save the outputs\n", - " n_retries=3\n", - ")" + "# uncomment to run the simulation\n", + "# dagres = gufe.protocols.execute_DAG(\n", + "# dag,\n", + "# shared_basedir=workdir,\n", + "# scratch_basedir=workdir,\n", + "# keep_shared=True, # set this to True to save the outputs\n", + "# n_retries=3\n", + "# )" ] }, { @@ -494,7 +495,7 @@ } ], "source": [ - "!ls shared_PlainMDProtocolUnit-6b85013e6cb94120baf447540650643b_attempt_0/" + "# !ls shared_PlainMDProtocolUnit-6b85013e6cb94120baf447540650643b_attempt_0/" ] }, {