Commit 71662d5e authored by Eliane Briand's avatar Eliane Briand 💯
Browse files

Added citations for published articles!

parent f4a859cd

content.en/_index.md

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@@ -36,14 +36,30 @@ This software package was made possible by work by members of the [Theoretical a 
If you find this software useful, please cite the following article:





- [Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications](https://pubs.acs.org/doi/10.1021/acs.jctc.4c01318)

- [Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation](https://pubs.acs.org/doi/10.1021/acs.jctc.4c01319)





```bibtex

[Citation information to be added upon publication]

```

@article{briand2024constant,

  title={Constant pH Simulation with FMM Electrostatics in GROMACS.(A) Design and Applications},

  author={Briand, Eliane and Kohnke, Bartosz and Kutzner, Carsten and Grubmüller, Helmut},

  journal={Journal of Chemical Theory and Computation},

  year={2024},

  publisher={ACS Publications}

}



@article{kohnke2024constant,

  title={Constant pH Simulation with FMM Electrostatics in GROMACS.(B) GPU Accelerated Hamiltonian Interpolation},

  author={Kohnke, Bartosz and Briand, Eliane and Kutzner, Carsten and Grubmüller, Helmut},

  journal={Journal of Chemical Theory and Computation},

  year={2024},

  publisher={ACS Publications}

}



### Preprints:



- [Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications](https://arxiv.org/abs/2410.01626)

- [Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation](https://arxiv.org/abs/2410.01754)

```





### Supplementary informations

content.en/docs/cph-postprocessing/analysis_tool.md

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| `--runfile`                | Path to the runfile from the titration script (`.yaml` file) |

| `--do_transition_count`    | Recommended: counts the transitions during the trajectory.              |

| `--output`                 | Path to the CSV file to be written, with the titration data |

| `--maxtime`                 | Consider data only up to the time (in ns) specified as argument.  |

| `--maxtime`                 | Consider data only up to the time (in ps) specified as argument.  |





Note that `--do_transition_count` slightly slows down the process, but is necessary to get accurate

content.en/docs/reference_list.md

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@@ -22,22 +22,18 @@ Here are the details of the publications cited in this site 
# Our most recent publications on FMM / constant pH









## Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications {#fmmcphA}



Authors: Eliane Briand, Bartosz Kohnke, Carsten Kutzner, and Helmut Grubmüller*

Authors: Eliane Briand, Bartosz Kohnke, Carsten Kutzner, and Helmut Grubmüller



(Preprint)

[https://arxiv.org/abs/2410.01626](https://arxiv.org/abs/2410.01626)

[https://pubs.acs.org/doi/10.1021/acs.jctc.4c01318](https://pubs.acs.org/doi/10.1021/acs.jctc.4c01318)



## Constant pH Simulation with FMM Electrostatics in GROMACS. (B) Design and Applications {#fmmcphA}



Authors: Bartosz Kohnke, Eliane Briand, Carsten Kutzner, and Helmut Grubmüller*

Authors: Bartosz Kohnke, Eliane Briand, Carsten Kutzner, and Helmut Grubmüller





(Preprint)

[https://arxiv.org/abs/2410.01754](https://arxiv.org/abs/2410.01754)

[https://pubs.acs.org/doi/10.1021/acs.jctc.4c01319](https://pubs.acs.org/doi/10.1021/acs.jctc.4c01319)





## A GPU-Accelerated Fast Multipole Method for GROMACS: Performance and Accuracy {#gpuFMM}