GROMACS Wizard - Computing in the Cloud#
This section is part of the GROMACS Wizard tutorial.
Use this page when you want to run the heavier GROMACS stages on cloud hardware instead of your local machine.
GROMACS Wizard allows you to launch cloud jobs for the NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulation steps. The screenshots below use the NVT Equilibration step as an example, but the same job-submission pattern applies to the other supported stages.
Before you start#
Before going further, first read the local workflow for the stage you want to run:
Before launching a computation in the Cloud, make sure that you have at least 1 computing credit in your SAMSON Connect account. You can check the number of credits you have in two ways:
- In SAMSON: open the Job manager (Interface > Job manager or Ctrl/Cmd + 6) and click the Show credits button.
- On SAMSON Connect: sign in and go to My account - you should see the number of credits you have on this page.
If you need credits, you can always buy them on SAMSON Connect: Buy computing credits.
Performing computations in the Cloud#
At this point, we assume that the input structure and simulation parameters are already defined.
Check the system#
This step is optional but recommended.
Before launching a computation in the Cloud, try to run the stage locally for a few tens or hundreds of steps to check for obvious issues. If your machine cannot run the job locally because the system is too large, click Generate inputs instead. This still validates part of the setup and can reveal common problems before you spend credits.
Create the job#
To launch computations in the Cloud, click the Equilibrate in the cloud / Simulate in the cloud button for the current stage. The machine-selection dialog lets you choose:
- the machine type
- the storage size
- the estimated cost of the machine and the storage
Only machine and storage costs are charged; file transfer is free.
Click the Open details button to see all the available machines: their characteristics and pricing. In the Performance column, you can see some hints. Click OK to close it.
For the tutorial and for testing, we recommend selecting the machine with 4 vCPUs and no GPU. It is the slowest (but cheapest) and is suitable for testing. Select this machine as shown in the image below.
Click OK to proceed.
Confirm the job#
Once you have chosen the machine and clicked OK, a security dialog appears to confirm the cloud launch. This dialog summarizes the job details, including the expected pricing.
In this dialog, you can also see how many computing credits remain in your account. Triggering a cloud job requires at least 1 credit to be available, but that does not mean that exactly 1 credit will be charged. It is only the minimum amount required to allow the job to start.
In this dialog, you can also modify the job's name, description, and add some notes.
Click OK to confirm the submission of the job to the Cloud.
Job initialization#
Once you confirm the job, SAMSON will open the Job manager and automatically start the job initialization. During the initialization process, the job files are automatically prepared and copied to the Cloud storage. Please make sure to check the Running checkbox in the top part of the job manager to display all the jobs that are being initialized or running. You can sort the jobs by various columns.
Note
You can open the Job manager anytime you want via Interface > Job manager or via shortcut Ctrl/Cmd + 6.
In the Job manager, the jobs are listed on the left. You can access the job's details by clicking the >> button (to hide the part with details, click the same button again). In this part, you can see all the details on your job: creation date, current progress, description, notes, pricing. In the image above, you can see the Progress part highlighted in green.
Start the job#
Once the job's initialization is finished and the job is ready to be started, a pop-up dialog will appear asking you to confirm the start. Click Yes.
Now, in the Job manager, you should see that the status of the job has changed to Starting. After a little moment, it should change again to Running.
In a moment, new messages should appear on the same line as the Progress indicators. Click the Events button to check them.
This will open the Job message history window. In this window, you should see the estimated date and time when the job will be finished. This is a time estimated by GROMACS. Please note that this time might be updated. For the system in the tutorial, the simulation in the Cloud in the slow testing machine will take about 10 minutes. Usually, for such systems, short simulations like these are faster to perform locally, but we launch in the Cloud for the sake of the tutorial.
While the computations are running in the Cloud, you can do other things in SAMSON or even close it - you will be able to access the jobs using the Job manager the next time you launch SAMSON. The job information is stored using the SAMSON Connect Cloud Service, and the job results will be stored in the Cloud storage.
Pausing or canceling a job#
While the job is running in the Cloud, you can always pause it or cancel it. To do so, choose the job from the job list and click on the associated option in the context menu. You can restart a paused job at a later time.
Completed job#
Once your job is completed, you will receive an email with a notification about that, as well as a new message in the Home > News inside SAMSON.
Open the Job manager (Interface > Job manager or Ctrl/Cmd + 6) and check your job in the job list - it should have the status Completed. Please make sure to check the Non-running checkbox in the top part of the job manager to display all the completed or canceled jobs. You can sort the jobs by various columns.
You can see the cost of the job (in computing credits) in the respective column (in the image above: 0.18).
In the job details, you should see that the Progress has changed to indicate that the job has finished.
In the job details, click the Events button to check for the messages. From the messages, we can also see that the job has finished successfully.
Download the results#
Now we can download the results of the computations from the Cloud.
To download the job's results, open the Job manager, double-click on the job or click Open result window in the job's context menu.
This will open the Job files window, allowing you to download the results and import them.
First, choose the download folder where you would like the job results to be downloaded. You can use the Copy button to copy the path to the resulting folder later.
You can use the Job files window to download results, in different ways:
- Download one or more files via their context menu (choose files and click Download in the context menu).
- Select files in the list and click the Download selection button.
- Download all files by clicking the Download all button.
We recommend downloading all the files since many of them are needed when processing the trajectory or importing results in SAMSON. Please note that the transfer of files is free.
Now, click the Download all button. This will start the download process - you can see the download status for each file in the associated column (see the image below).
The job files that were not downloaded will still be available next time you launch SAMSON - the results are stored in the Cloud storage. Once you have downloaded all results and you no longer need to keep them in the Cloud, we recommend deleting the job and its files (see below in the Delete job section).
Once a file has been downloaded, you can access various commands in its context menu.
Show in folder - opens the folder with the file in the default file explorer of your OS.
Open - opens the file using the associated viewer in your OS, it is useful for opening text files (e.g. txt, log).
Import - imports the file in SAMSON, it is applicable to all the files which can be opened in SAMSON, e.g. gro, xtc, trr, pdb.
Copy folder path - copies the path to the folder containing the file to the clipboard.
Copy file path - copies the path to the file to the clipboard.
The latter command is useful, for example, to copy a path to the resulting GRO file to set it as the Input structure for the next step.
Import results in GROMACS Wizard#
Once the results are downloaded, you can import them in GROMACS Wizard.
In the Job files window, click the Copy button to copy the path to the folder with results.
Now, in GROMACS Wizard, go to the tab associated with the job, e.g. for this NVT Equilibration job go to the Equilibrate (NVT) tab and click the associated Import (*) results button.
This will open a dialog where you will need to choose the folder from which you would like to import results. Paste the path you copied just before. This should immediately show the list of files that will be imported. Click OK to import the trajectory and create plots.
Depending on the step (equilibration or production molecular dynamics simulation), there might be various pop-up dialogs asking for plotting and trajectory importing options - please see the associated NVT Equilibration, NPT Equilibration, Production Molecular Dynamics Simulation sections on importing results for more information. In the image below, you can see an example of a trajectory import dialog. Click OK if you would like to import the trajectory.
This will load the trajectory as chosen by you and will generate plots depending on the step.
You can apply a visual preset of your choice (Biology > Visual preset) or apply visual models directly.
Delete the job#
Once you download results and you no longer need the job files to remain in the Cloud, you can delete the job using the Job manager.
The job results are stored in Cloud storage and while the storage price is very low, we recommend deleting the jobs that you no longer need because the storage cost will start to be deducted from your computing credits after some time. You can see the storage cost in the job's details in the Job manager.
To delete a job, open the Job manager, choose among the jobs the one that you would like to delete, right-click on it, and press Delete in the job's context menu.
A pop-up dialog will appear asking you to confirm the action. Click OK if you really want to delete the job.
In a moment, the job should be deleted and removed from the jobs list, but you might still be able to see the job's details on the right side of the Job manager - there you can see in the Progress that the job has been deleted (or is still in the process of being deleted), you can click Details to see more detailed information.
Need Help?#
Have questions or feedback? Feel free to reach out via the Forum, via e-mail, via the Feedback button in SAMSON, or by directly discussing with us.