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AMBER: Difference between revisions
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[https://ambermd.org/ Amber] is the collective name for a suite of programs that allow users to perform molecular dynamics simulations, particularly on biomolecules. None of the individual programs carry this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. | [https://ambermd.org/ Amber] is the collective name for a suite of programs that allow users to perform molecular dynamics simulations, particularly on biomolecules. None of the individual programs carry this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. | ||
== Amber vs. AmberTools == | == Amber vs. AmberTools == <!--T:20--> | ||
We have modules for both Amber and AmberTools [[Available software|available in our software stack]]. | We have modules for both Amber and AmberTools [[Available software|available in our software stack]]. | ||
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* The [https://ambermd.org/AmberTools.php AmberTools] (module <code>ambertools</code>) contain a number of tools for preparing and analysing simulations, as well as <code>sander</code> to perform molecular dynamics simulations, all of which are free and open source. | * The [https://ambermd.org/AmberTools.php AmberTools] (module <code>ambertools</code>) contain a number of tools for preparing and analysing simulations, as well as <code>sander</code> to perform molecular dynamics simulations, all of which are free and open source. | ||
* [https://ambermd.org/AmberMD.php Amber] (module <code>amber</code>) contains everything that is included in <code>ambertools</code>, but adds the advanced <code>pmemd</code> program for molecular dynamics simulations. | * [https://ambermd.org/AmberMD.php Amber] (module <code>amber</code>) contains everything that is included in <code>ambertools</code>, but adds the advanced <code>pmemd</code> program for molecular dynamics simulations. | ||
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To see a list of installed versions and which other modules they depend on, you can use the [[Using modules#Sub-command_spider|<code>module spider</code>]] command or check the [[Available software]] page. | To see a list of installed versions and which other modules they depend on, you can use the [[Using modules#Sub-command_spider|<code>module spider</code>]] command or check the [[Available software]] page. | ||
==Loading AmberTools 21== | ==Loading AmberTools 21== <!--T:23--> | ||
Currently, AmberTools 21 is available on all clusters. | Currently, AmberTools 21 is available on all clusters. | ||
=== Non-GPU version === | === Non-GPU version === <!--T:24--> | ||
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 ambertools/21 | <!--T:25--> | ||
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 ambertools/21 | |||
source $EBROOTAMBERTOOLS/amber.sh | source $EBROOTAMBERTOOLS/amber.sh | ||
<!--T:26--> | |||
Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, and sander.OMP | Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, and sander.OMP | ||
=== GPU version === | === GPU version === <!--T:27--> | ||
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 ambertools/21 | <!--T:28--> | ||
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 ambertools/21 | |||
source $EBROOTAMBERTOOLS/amber.sh | source $EBROOTAMBERTOOLS/amber.sh | ||
<!--T:29--> | |||
Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, sander.OMP, sander.quick.cuda, and sander.quick.cuda.MPI | Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, sander.OMP, sander.quick.cuda, and sander.quick.cuda.MPI | ||
==Loading Amber 20== | ==Loading Amber 20== <!--T:30--> | ||
Currently, Amber20 is available on all clusters. | Currently, Amber20 is available on all clusters. | ||
=== Non-GPU version === | === Non-GPU version === <!--T:31--> | ||
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20.9-20.15 | <!--T:32--> | ||
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20.9-20.15 | |||
<!--T:33--> | |||
Provides all MD programs available in AmberTools/20 plus pmemd (serial) and pmemd.MPI (parallel). | Provides all MD programs available in AmberTools/20 plus pmemd (serial) and pmemd.MPI (parallel). | ||
=== GPU version === <!--T:11--> | === GPU version === <!--T:11--> | ||
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15 | <!--T:34--> | ||
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15 | |||
<!--T:35--> | |||
Provides all MD programs available in ambertools/20 plus pmemd (serial), pmemd.MPI (parallel), pmemd.cuda (single GPU), and pmemd.cuda.MPI (multi - GPU) | Provides all MD programs available in ambertools/20 plus pmemd (serial), pmemd.MPI (parallel), pmemd.cuda (single GPU), and pmemd.cuda.MPI (multi - GPU) | ||
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module load gcc/5.4.0 openmpi/2.1.1 amber/18.10-18.11 scipy-stack/2019a | module load gcc/5.4.0 openmpi/2.1.1 amber/18.10-18.11 scipy-stack/2019a | ||
=== GPU versions === | === GPU versions === <!--T:36--> | ||
<!--T:12--> | <!--T:12--> | ||