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| align="center" | [http://www.gromacs.org gromacs-plumed] | | align="center" | [http://www.gromacs.org gromacs-plumed] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 2018.1, 2019.5, 2019.6, 2021.2, 2021.4, 2021.6, 2022.3 | | align="center" | 2018.1, 2019.5, 2019.6, 2021.2, 2021.4, 2021.6, 2021.7, 2022.3 | ||
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div> | | Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [http://www.plumed-code.org plumed] | | align="center" | [http://www.plumed-code.org plumed] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 2.3.7, 2.4.2, 2.4.3, 2.5.2, 2.5.3, 2.5.4, 2.6.1, 2.6.2, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.8.1 | | align="center" | 2.3.7, 2.4.2, 2.4.3, 2.5.2, 2.5.3, 2.5.4, 2.6.1, 2.6.2, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.7.6, 2.8.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. This module has been compiled with additional modules, and support for XDR-files (GROMACS XTC/TRR), Python, GSL, Boost-serialization, Boost-Graph and other optional features. To find out more, run 'plumed config show' after loading this module. Homepage: http://www.plumed-code.org URL: http://www.plumed-code.org Keyword:chem<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. This module has been compiled with additional modules, and support for XDR-files (GROMACS XTC/TRR), Python, GSL, Boost-serialization, Boost-Graph and other optional features. To find out more, run 'plumed config show' after loading this module. Homepage: http://www.plumed-code.org URL: http://www.plumed-code.org Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0 | | align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4.57, Text::NSP-1.31 Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://triqs.github.io/triqs triqs] | | align="center" | [https://triqs.github.io/triqs triqs] | ||
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| align="center" | chem | | align="center" | chem | ||
| align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1 | | align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: ase-3.22.1, Pint-0.19.2, pydantic-1.9.1, qcelemental-0.24.0, xtb-6.5. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: ase-3.22.1, Pint-0.19.2, pydantic-1.9.1, qcelemental-0.24.0, xtb-6.5.1 Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [https://github.com/xtensor-stack/xtensor xtensor] | | align="center" | [https://github.com/xtensor-stack/xtensor xtensor] | ||