AMBER Set-Up

This directory contains a collection of scripts for preparing systems and running simulations with AMBER MD.

Berendsen

This directory contains scripts that use the Berendsen thermostat.

mineq.sh is a script for looping through minimization to equilibration using CPUs. It calls mdin.1 through mdin.10. dynamicsgpu.sh uses GPUs for production. It calls mdin.11.

You can read more about what's happening in mdin.1 to mdin.11 at: https://emleddin.github.io/comp-chem-website/AMBERguide-example-files.html#NVT

Langevin

This directory contains scripts that use the Langevin thermostat.

hedi-NPT-NVT

mineq.sh is a script for looping through minimization to equilibration using CPUs. It calls mdin.1 through mdin.3. dynamicsgpu.sh uses GPUs for production. It calls mdin.4.

You can read more about the mdin files in the hedi-NPT-NVT subfolder at: https://emleddin.github.io/comp-chem-website/AMBERguide-example-files.html#NVT-NPT

miller-NPT

SLURM-jobfile is a jobfile built for running AMBER on an XSEDE resource. Each of the mdin files can be renamed numerically, if you wish to use a combination of ../hedi-NPT-NVT/mineq.sh and ../hedi-NPT-NVT/dynamicsgpu.sh.

You can read more about the mdin files in the miller-NPT subfolder at: https://emleddin.github.io/comp-chem-website/AMBERguide-example-files.html#NPT

submission-scripts

This directory contains scripts for running SLURM jobs on SDSC's Comet or UNT's Talon.

system-preparation

This directory contains scripts for preparing the biomolecular structure for MD.