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AMBER: Difference between revisions
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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 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. | ||
==Running Amber 18== | ==Running Amber 18== <!--T:8--> | ||
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Currently, versions 18 and 18.10-18.11 are available on all clusters. | Currently, versions 18 and 18.10-18.11 are available on all clusters. | ||
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Non-GPU versions | Non-GPU versions | ||
module load gcc/5.4.0 openmpi/2.1.1 amber/18 scipy-stack/2019a | module load gcc/5.4.0 openmpi/2.1.1 amber/18 scipy-stack/2019a | ||
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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 | ||
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GPU versions: | GPU versions: | ||
module load gcc/5.4.0 cuda/9.0.176 openmpi/2.1.1 amber/18 scipy-stack/2019a | <!--T:12--> | ||
module load gcc/5.4.0 cuda/9.0.176 openmpi/2.1.1 amber/18 scipy-stack/2019a | |||
or | or | ||
module load gcc/5.4.0 cuda/9.0.176 openmpi/2.1.1 amber/18.10-18.11 scipy-stack/2019a | module load gcc/5.4.0 cuda/9.0.176 openmpi/2.1.1 amber/18.10-18.11 scipy-stack/2019a | ||
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[name@server $] module load amber/16 | [name@server $] module load amber/16 | ||
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This version does not support some Python functionality of Amber. | This version does not support some Python functionality of Amber. | ||
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For a general discussion about submitting jobs, see [[Running jobs]]. | For a general discussion about submitting jobs, see [[Running jobs]]. | ||
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In examples below, change the module load command to one above if you with to use the newer version. | In examples below, change the module load command to one above if you with to use the newer version. | ||