[Yohsuke Fukai]

Hello, I am trying to use GENESIS for a coarse-grained scale simulation with AICG2+, 3SPN.2C, and custom force fields. I found the forcefield set to RESIDCG in the tutorial, but could not find its role in the documentation. Is it documented somewhere? If not, would you mind providing us with a quick explanation for what this parameter does?

[ctan]

Hi Fukai-san, thanks for reporting this problem of our documentation. We are very sorry for providing the flawed user manual on the website.

 

Right now we have just uploaded a new version to the “Download” page. Would you please download the doc again from https://www.r-ccs.riken.jp/labs/cbrt/genesis-version-1-7/

 

Many of the residue-level CG model related options can be found in section 6.7 “Residue-level coarse-grained models”. Please let us know if you have further questions on this topic.

 

Thanks!

[Yohsuke Fukai]

Hi, thank you for your reply Tan-san! The documentation will be quite useful.

Sorry for the additional question, but is there any method to simulate a system with a custom force field (for example, just Lennard-Jones with specific residue-dependent interactions)? According to the documentation, I understood RESIDCG accepts specific types of interaction models.

[ctan]

I’m sorry to say that custom force fields such as LJ potentials with user-defined parameters have not been fully supported yet. Specifically, RESIDCG only works for some fixed types of interactions, although users do have some freedom of choosing different combinations of available CG models. We actually agree that custom interactions should be an important function of MD programs, and we will consider this as a future direction of GENESIS development.

For the time being, if the potential functions you are considering are “standard” ones, maybe a workaround is to play with the existing all-atom force fields, with some hacking. For example, you can write simple topology and coordinate files in the GROMACS format and run simulations with those files in GENESIS (forcefield = GROAMBER).

[Yohsuke Fukai]

Thank you again for your clear explanation! I’ll definitely try that option. I’m also looking forward to future development in this direction!