gmx_MMPBSA
gmx_MMPBSA copied to clipboard
Valdes-Tresanco-MS
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
### In which tool? _No response_ ### New Feature - [ ] Add support for pbsa.cuda ### Description Install pbsa.cuda as follows: Line 37 run.cmake file in amber20_src/build: ``` #...
### In which tool? gmx_MMPBSA ### New Feature Implement the PB calculation from APBS ### Description _No response_ ### Relevance medium ### Difficulty to implement medium
- [ ] namd support [low priority] - [ ] amber support [medium priority]
### In which tool? gmx_MMPBSA ### New Feature In addition to the number for the index group selection, allow the string for the group. For instance, instead of group 0,...
Practically, the generation of topologies using tLeap is unnecessary since the conversion with ParmEd works perfectly. It also makes the code more complex, making it difficult to implement new functions....
### In which tool? gmx_MMPBSA ### New Feature Support explicit water molecules in gmx_MMPBSA calculations ### Description _No response_ ### Relevance low ### Difficulty to implement low
Create an `*.mdin` to compute the rest of the energy components with `sander` and a `*.mdin` for `GBNSR6`. **Note:** _The `*.mdin` of GBNSR6 must have the `namelist` starting from the...
Currently, we have a docker container thanks to @vsdepontes. However, we haven't added it to the documentation yet. I will open this issue exclusively for it _Originally posted by @vsdepontes...
Plotly is a fairly robust web plotting tool. Advantage: - Generate very cool graphics, both static images, and interactive graphics. - Allows saving in the same formats as matplotlib -...
Metadata
Owner
Metadata
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.