Good day everyone! I am a Biochemistry undergraduate in the Philippines and to be very honest, we have no background in bioinformatics since we really focused on wet lab techniques + theory. Due to the pandemic crisis, no one in our batch can research on topics that require lab experiments. So we're all stuck learning something new on our own, which is something purely computational.
Another expert here suggested I use CHARMM GUI Polymer Builder for my input files for Gromacs, but the installer I have for Gromacs simply won't work (I have a Windows 10 laptop and it requires Ubuntu 20.04 LTS installment so that I could install Gromacs, but the Ubuntu won't launch). I have access to HPC so I'm asking if my input files from CHARMM would work? If yes, can you provide me with resources/tutorials on how I could write a job script for it?
Thank you so much!
Hi Max,
To access in HPC I did following things.
1. I made sure the gromacs version available in HPC (mine gromacs/2018.4);
2. for gromacs code: When we generate input files in Charmmgui, it generates Readme file in 'Gromacs' folder). It has all the codes to run just we need to correctly assign your HPC resources. What kind of job scheduling you have in HPC ? eg. PBS, SBATCH etc.
Susheel Pangeni Hello Susheel, we have SLURM in HPC
I have copy + pasted the script found in README but the job failed because it was telling me that the "topol" file was not found even though I have placed it in the folder, and "step4.0_minimization.gro" file was not found although I just copy + pasted the files from the CHARMM input files.
Before I sent these scripts, I made sure I fixed the DOS and UNIX line breaks since I am using a Windows 10 laptop.
Images attached are the script from README file, and the .err sent by the SLURM job scheduler.
Thank you so much!
Hi Max Tolentino ,
Make sure you have gromacs installed in HPC , and also csh (look at the readme script there is bin/csh in the first line so you need csh in bin folder). Now enter ./readme. If it does not work you have to search why this failed from the first command in the script (which is nothing but assembly of gromacs commands). *For my case I have to modify gmx_d to gmx in step 4.0 minimization.
Does this help?
Regards
Anirban :)
Hello Sir Anirban Paul !
I've read the "README" file from the CHARMM input files but it's been over a week of my attempting to successfully run a job in SLURM HPC (the time-consuming part is the queueing, which takes almost half a day).
Attached are the job script, the .err file I received, and the side-by-side windows of my CHARMM input files and SLURM folder.
Thank you so much!
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