Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix issue #291 #292

Merged
merged 1 commit into from
May 17, 2024
Merged

Fix issue #291 #292

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 11 additions & 4 deletions nodes/playground/prepareFEP.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -317,7 +317,10 @@
")\n",
"# Create a composite system\n",
"system1.removeMolecules(lig1)\n",
"system1.addMolecules(merged)"
"system1.addMolecules(merged)\n",
"# Make sure the box vectors are in reduced form.\n",
"system1.reduceBoxVectors()\n",
"system1.rotateBoxVectors()"
]
},
{
Expand All @@ -336,7 +339,11 @@
" \"merged_at_lam0.pdb\",\n",
" merged,\n",
" \"PDB\",\n",
" {\"coordinates\": \"coordinates0\", \"bond\": \"bond0\", \"element\": \"element0\"},\n",
" property_map={\n",
" \"coordinates\": \"coordinates0\",\n",
" \"bond\": \"bond0\",\n",
" \"element\": \"element0\",\n",
" },\n",
")\n",
"if is_somd2:\n",
" BSS.Stream.save(system1, root)\n",
Expand Down Expand Up @@ -426,9 +433,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.11"
"version": "3.12.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
9 changes: 8 additions & 1 deletion nodes/playground/prepareFEP.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -258,6 +258,9 @@ def loadMapping(mapping_file):
# Create a composite system
system1.removeMolecules(lig1)
system1.addMolecules(merged)
# Make sure the box vectors are in reduced form.
system1.reduceBoxVectors()
system1.rotateBoxVectors()


# In[ ]:
Expand All @@ -273,7 +276,11 @@ def loadMapping(mapping_file):
"merged_at_lam0.pdb",
merged,
"PDB",
{"coordinates": "coordinates0", "bond": "bond0", "element": "element0"},
property_map={
"coordinates": "coordinates0",
"bond": "bond0",
"element": "element0",
},
)
if is_somd2:
BSS.Stream.save(system1, root)
Expand Down
Loading