Problem running gromacs simulation

MDWeb
22

Hi,

we would need to see the yaml file with the input parameters to find out what is the problem. Could you please attach it?

First thing to check is the mdp file used in the step24_grompp_md: Preprocess long MD simulation after setup, which is the one defining the length of the production MD.

23

Here it is.

(Attachment workflow_input_descriptions.yml is missing)

24

Where can I find the yaml files? When I download the scripts, these files appear. I tried to attach the .yml file but the system didn’t allow me to attach this type of file.

Untitled.jpg

25

We need the workflow.yml file. Just rename it to workflow.yml.txt and try to upload it again please.

26

Thanks.

workflow.yml.txt (7.47 KB)

27

Can you please tell us how you are running the workflow?

28

You mean the settings? I wanted to run the gromacs md simulation with a total time of 100ns, output freq of 500, time step of 2 and 300k temperature. Other settings were set as default. Amber99sb protein for forcefield and tip3p water model.

29

What I wanted to know if you had run the workflow in your own premises or using the website. Looking at the log you attached, I see the workflow run till the step24_grompp_md: Preprocess long MD simulation after setup. The tpr generated by this last step of the workflow should then be used to run the long MD simulation in your own premises. All this is explained in the corresponding help section.

So if you are still interested in the 100ns trajectory, you could follow the steps explained. BioBB_wfs infrastructure can help in the setup process and in the generation of the files and steps that you need to run a MD simulation, but is not designed to run hundreds of nanoseconds, as it would require a non-negligible amount of computational power.

Besides, the setup workflow you run (the one producing the log file you attached) is actually running 500ps of free (unrestrained) simulation, not 50ns as you said before. Please read carefully the help pages for the desired workflow, everything is explained there. For example, here is clearly stated that the last step of the setup workflow (Free -unrestrained- Molecular Dynamics Simulation) runs 500ps (not 50ns!).