lenhanpham / MoSu-CHARMM

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MoSu-CHARMM

MoSu-CHARMM force field developed and reported in the paper "Predicting Biomolecule Adsorption on MoS₂ Nanosheets with High Structural Fidelity" https://doi.org/10.1039/D1SC06814H can be obtained here. The force field is ready for use. I'll spend a bit more time to write instruction on how to use MoSu-CHARMM. Basically, MoSu-CHARMM was developed to be used with GROMACS, and therefore can be used with the command gmx pdb2gmx.

Since several new atomtypes have been newly introduced in MoSu-CHARMM, the gmx pdb2gmx might not cover all bond types, angle types, and dihedral types. You might want to manually add these bonded paramters to MoSu-CHARMM to make it work for your proteins and peptide chains. You can give me a message, and then I can add all new bonded parameters for your case.

MoSu-CHARMM can work with all types of organic compounts as well.

Usage of MoSu-CHARMM Force Field

MoSu-CHARMM is a high-fidelity force field for simulation interaction between biomolecules (peptides and proteins) & all possible organic compounds and the MoS2 surface in aqueous media. MoSu-CHARMM can be used for gas-phase simulation as well. In order to use MoSu-CHARMM in aqueous media, the TIPS3P water model should be used. Parameters for description of interaction between water and MoS2 can be found in another publication "Pham, L. N.; Walsh, T. R. Force Fields for Water–Surface Interaction: Is Reproduction of the Experimental Water Contact Angle Enough? Chem. Commun. 2021, 57 (27), 3355–3358. doi:10.1039/d1cc00426c". All parameters in the Chem. Sci. paper, together with parameters in the Chem. Comm. one, make MoSu-CHARMM complete.

*Users need to pay attention to setting parameters such as vdw cutoff and rcoulomb when using MoSu-CHARRM. These parameters are mentioned in two papers above.

Please cite these two publications if you use MoSu-CHARMM in your works

1. "Pham, L. N.; Walsh, T. R. Force Fields for Water–Surface Interaction: Is Reproduction of the Experimental Water Contact Angle Enough? Chem. Commun. 2021, 57 (27), 3355–3358. doi:10.1039/d1cc00426c".

2. Pham, L. N.; Walsh, T. Predicting Biomolecule Adsorption on MoS2 Nanosheets with High Structural Fidelity. Chem. Sci. 2022 doi:10.1039/D1SC06814H