hello, i am trying to run molecular dynamics throug MDweb server , i succesfully generated the files for md set up using Gromacs MD full set up, i am trying to generate nvt and npt but i couldn’t successfully run… how to solve this issue…
I’m afraid MDWeb will not be able to handle your request, as the generated system is far too large for the web server. Your structure is long (~200 Angstroms end-to-end), resulting in a huge box, with ~1 million atoms. Although MDWeb is able to run the preparation (setup), it is not able to extract the results and use them back for NVT or NPT run, due to HTTP read timeouts.
That said, I would recommend you to take a look at the BioExcel Building Blocks (biobb) website, which is a more recent library that can help you on the MD setup and run processes. You could try to run a setup with your structure using the Protein MD Setup workflow here.
Thanks for your interest in our tools!
Thank you sir…