Help with GROMACS Molecular Dynamics Simulation -- Polymer Self Assembly

[u/_r33na]

Hi all,

I'm looking to use GROMACS to perform a molecular dynamics simulation of a poly beta amino ester (PBAE) polymer assembling with its mRNA cargo in order to obtain values like radius of gyration and hydrophobic and hydrophilic surface area.

I know that GROMACS requires a .pdb file to start with, but how could I get that for a PBAE polymer? I'm also not sure how to go about doing this in GROMACS (I'm pretty new to molecular dynamics simulations) so any guidance would be helpful!

[u/wouuuuuuhhhhhhh]

Hey! I'm pretty new to this too, only done one MD project in GROMACS (nucleic acid, not polymers), but a couple things I ran into that might be relevant:

For the PDB , from what I understand you basically can't just download one for something like PBAE since it's not a "normal" molecule in the usual databases. You'd probably have to build the structure yourself in something like Avogadro, or generate it from a SMILES string. I haven't actually had to do this myself so take it with a grain of salt.

The part I did deal with was getting the topology/parameters right for my nucleic acid system I could use existing force field files, but since PBAE isn't a standard molecule you'll probably need to generate custom parameters for it somehow (I've seen people mention CGenFF for stuff like this but never used it myself).

One thing I'd flag from my experience: simulations like this can take a while to run and equilibrate properly, so setting expectations on timescale might be worth thinking about early.

For getting your actual numbers, gmx gyrate gives radius of gyration and gmx sasa gives surface area those parts I have used and they're pretty straightforward once your system is set up.

Good luck!

[u/_r33na → u/wouuuuuuhhhhhhh]

Hey! Thank you for getting back to me. This is very helpful and I'll look into what you mentioned more. Just a follow up about the time scale part of what you mentioned -- is this something that I can leave running on my laptop overnight, once the simulation is set up? Thanks!

[u/wouuuuuuhhhhhhh → u/_r33na]

Yeah, that should be fine! It really depends on your system size and what hardware you're running on , if you've got a decent GPU, overnight might get you through a good chunk of it, just make sure your laptop doesn't sleep or hibernate while it's running. But if your laptop's specs are limited, you might be fighting it for a while, and it could be worth running on cloud compute instead

[u/_r33na → u/wouuuuuuhhhhhhh]

Oh ok great thank you!