Local simulations #23
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ese include several runs that vary simulation timestep from 3 to 2 fs
…om for metadynamics simulations
…imize the system in vaccum, and solvate the system
…lude REMD setup scripts
…ly from the first trajectory. Reran clustering on some terphenyl tetramers
… and analysis script to cluster output trajectory
…etad simulation running, might need some adjustments in the form of an input file
…ion to select whether things are run on a cluster or locally. Essentially just specifying whether or not to run with mpirun or just use a GMX executable
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I think there should be a set of scripts to also run simulations on local computers. This is obviously less feasible with large parallel systems like REMD or MW MetaD simulations, however for single simulations local computers with NVIDIA GPUs can easily achieve useful simulation speeds necessary to finish ~100 ns in a couple of hours.