Try using AMBER99SB

Hi,

There is no best or worst forcefield, as different ff has been developed with specific goal in mind. I have seen a wide variety of ff in literature, so in most cases it is just personal preference.

However, Amber and Charmm are suitable for this purpose. AMBER99sb-ildn is better and inherently available in gromacs.

For further reading, you can consult the following paper (and other similar papers):

https://www.pnas.org/content/115/21/E4758

Best.,

These days both Amber and CHARMM have more dedicated FFs to treat disordered regions. The "bare" Amber99SB, even with ILDN, is not guaranteed to produce meaningful results for IDPs/IDRs.

DE Shaw's group published their 'disp' correction that was recently made available for Gromacs by Paul Robustelli: https://github.com/paulrobustelli/Force-Fields (you might need to switch to their version of TIP4P to get optimal performance, though).

In parallel, CHARMM's version 36m was specifically designed to improve the treatment of IDRs: https://www.charmm.org/charmm/showcase/featured-research/charmm36m-an-improved-force-field-for-folded-and-intrinsically-disordered-proteins/

You will find ample of publications on simulations for protein having both structured and disordered states defining CHARMM or AMBER as a better choice.

Regards

You may also try OPLS-AA, which has better balance between ordered and disordered structures.