Change GROMACS output to Interchange #17
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JHoeflich1
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Aug 22, 2025
JHoeflich1
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JHoeflich1
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Requesting a small change when adding POSRES section to the topology. Other than that everything works great!
| sect = 'water' | ||
| if match_string in line: | ||
| if mol == 1 and insert_string not in contents_orig[index - 1]: | ||
| temp_file.write(insert_string) |
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There is a small bug here where the #ifdef POSRES block gets inserted in multiple [ moleculetype ] sections.
A simple fix (beginning at like 825) is:
mol = 0
posres_inserted = False # Add
for index, line in enumerate(contents_orig):
if 'HOH' in line:
sect = 'water'
if match_string in line:
if mol == 1 and not posres_inserted: # Add
temp_file.write(insert_string)
posres_inserted = True # Add
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Description
Change GROMACS file output to interchange to ease code maintanence and prevent the need for outside tools. Interchange by default does not include the settles parameters for each water model, so we manually add these parameters for 3-point water models. We will need to expand to include parameters for 4-point water models in the future.
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