Fetching latest commit…
Cannot retrieve the latest commit at this time.
|Failed to load latest commit information.|
AmberGPUMDSimulation Version 1.1 Purpose Molecular dynamics (MD) simulations are electronic microscopes that allow researchers to study atomic details of biological systems (1). Applying Newton’s laws of motion, MD simulations can predict atom movements following a time series. MD simulations usually involve four steps: minimization, heating, equilibration, and production, and the purpose of this Amber GPU MD simulation workflow is to automate these processes using graphics processing units (GPUs). This workflow can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. MD simulations simulate atomic movements to help scientists predict reaction mechanisms, identify druggable pockets, and understand allosteric regulation (1). Moreover, due to the simple nature of this workflow, the workflow can be used as a starting point for learning how to run MD simulations. It can also be used a starting point developing workflows that involve more complicated aspects MD. It is our hope that this workflow will enable improved dissemination and reproducibility in the field of molecular dynamics. Parameters ExecutionChoice This parameter gives the option to run same workflow either on a local machine or in a GPU cluster. NP The number of CPU processors for the minimization steps. It is the same number of processors for each of the step. CMPD The folder name containing the topology and coordinate files. The folder name needs to match the stem name of the topology and coordinate file. AMBERHOME_local $AMBERHOME/bin on your local machine. This should be the path that points to where pmemd.MPI is located. inputFolder The inputFolder path on your local machine. It is the directory where the confDir and CMPD folder is located. An absolute path is required. TargetHost The remote cluster login. IdentityFile The identity file (id_rsa) that allows remote access. A complete and absolute path is required. remoteDir Work Directory on remote GPU cluster. A complete and absolute path is required. numOfJobs This parameter will allow "n" production jobs to be submitted in parallel for a single system. This parameter is only for job submissions in GPU clusters AMBERHOME_cpu $AMBERHOME on remote cluster on CPU nodes. AMBERHOME_gpu $AMBERHOME on remote cluster on GPU nodes. cpuModulesToLoad Modules dynamically modifies a user’s execution environment to configure the shell for an application. gpuModulesToLoad The parameter “gpuModulesToload” prepares execution environment on GPU nodes on a cluster. t-cpu Time requests for each of the minimization step in the remote cluster. t-gpu Time requests for the heating step, equilibration steps and production step in the remote cluster. Input & Output The input for this workflow is a set of directories include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, etc. Sample inputs and outputs are available and included as a part of the download. They are in the inputs and outputs folders, respectively. Operating System Requirment Linux Caution An extensive user guide/manual comes along with this workflow. For any question, please consult the manual. Also, there is an appendix section at the end of the maunaul where it answer some of the questions users may have if the workflow fails to run.