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projects:tauramddescription [2020/07/21 13:30] kokhadmin [RAMD and its applications (using the implementation in Gromacs) are described in:] |
projects:tauramddescription [2020/07/21 14:53] wade [Tutorial on application of RAMD] |
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| - | =====Tutorial on application of RAMD===== | + | =====Tutorials on the application of RAMD===== |
| === Implementation in NAMD === | === Implementation in NAMD === | ||
| - | A tutorial describing the [[https://www.h-its.org/downloads/ramd/|τRAMD]] process of setting up and running RAMD simulations in NAMD for estimation of the relative residence time (τ) of a protein-small molecule complex can be found ;[[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-namd/|here.]] | + | A tutorial describing the τRAMD process of setting up and running [[https://www.h-its.org/downloads/ramd/|RAMD]] simulations in NAMD for estimation of the relative residence time (τ) of a protein-small molecule complex can be found [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-namd/|here.]] |
| === Implementation in GROMACS === | === Implementation in GROMACS === | ||
| - | A tutorial describing the [[https://github.com/HITS-MCM/gromacs-ramd|τRAMD]] process of setting up and running RAMD simulations in GROMACS for estimation of the relative residence time (τ) of a protein-small molecule complex can be found [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/||here]]. | + | A tutorial describing the τRAMD process of setting up and running RAMD simulations in GROMACS for estimation of the relative residence time (τ) of a protein-small molecule complex can be found [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/|here]]. |
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| === τRAMD === | === τRAMD === | ||
| - | τ-random acceleration molecular dynamics (τRAMD) is a protocol based on the RAMD method for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanism. [[https://www.h-its.org/downloads/ramd/|Read more]] | + | τ-random acceleration molecular dynamics (τRAMD) is a protocol based on the RAMD method for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanism. An introduction to the method is given [[https://youtu.be/kCUyQtoo4cE|here]] |
