May I ask everyone, I would like to do multiple ssDNA fitting, one of which has a secondary structure of 200 nt, and the others ranging from 20 to 40 nt? Do we need to minimize their respective energies before simulating them together? I am a beginner who has just started working in this field and has little knowledge about GROMACS. I have completed the beginner’s tutorial on lysozyme in water. If you could leave some valuable guidance, I would be extremely grateful.
What is the purpose of the fitting, finding plausible base pairings? Do the molecules already have a secondary structure? A 200-nt ssDNA is unlikely to fold in an all-atom FF, perhaps in a coarse-grained one such as Martini or 3SPN.2C. Deep learning models such as RoseTTAFold2NA might be able to create reasonable models too (this one includes protein generation, perhaps there are smaller models for dsDNA that do the job too).
If you’re convinced that you need to run a fully atomistic MD simulation of a large ssDNA, then you’re better off with the DESRES force field.
Ah, by the way, please don’t ask questions in Site feedback, move this to User discussions.
Thank you for all your suggestion !!! It’s useful and I realize that I didn’t describe my question clearly . I will ask this question in User discussion in detail and delete this page in 12 hours .
Actually, this 200 nt ssDNA strand has a hairpin structure, and I want to analyze which key bases are involved in the hybridization of the complementary 20 nt ssDNA with it to form dsDNA.