added a new tool with an accessory python script, and also modified the macros.xml file #137
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| </inputs> | ||
| <outputs> | ||
| <data name="output1" format="gro" from_work_dir="./multiples.gro" label="GROMACS new structure with inserted-molecules (GRO) on ${on_string}"/> | ||
| <data name="output2" format="txt" from_work_dir="./addedmols.txt" label="Total number of molecules succesfully added on ${on_string}"/> |
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Not really convinced about this, I guess the idea is that the user modifies the top file themselves? It would be nice if we could do this as part of the tool.
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Hey Simon,
We were originally going to make this an all-in-one tool, but we decided to keep it as the standard gmx tool. We are working on a separate "add topologies" tool which will add topologies for inserted molecules, water, NaCL, and everything else. This output containing the number of added molecules would then be used as an input in the next step of adding topologies.
The reason why this is necessary is because not all systems can be setup via the GROMACS initial setup tool (not all force fields are present in gromacs, which leads to unrecognized residue and atom types depending on your system). So having a separate tool that adds topologies will allow versatility for users.
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If I understand this correctly, the addedmols.txt will just contain a single integer, with the same value as the nmols parameter? If so, I don't think this is useful, I think the user can take care of this parameter themselves and remembering to use the same value for both tools.
…g a problem passing test on github
Added a new gromacs tool, gmx insert-molecules. This will allow users to insert many copies of a molecule into a system, using only its .gro file. This tool has many uses, including setting up systems with non-water solvents and adding non-standard solutes (such as complex ions). Virtually any structure with a .gro file can become an inserting molecule. Cheers!