Comment on "Martini force field for protonated polyethyleneimine". Issue 4 (20th November 2020)

• Record Type: Journal Article
• Authors: Mahajan, Subhamoy; Tang, Tian
• Is Part Of: Journal of computational chemistry. Volume 42:Issue 4(2021)
• Page Start: 261
• Page End: 263
• Publication Date: 2020-11-20
• Subjects: Martini -- coarse‐grained model -- polyethylenimine; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.26453
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract: We comment on the recently published Martini forcefield for linear polyethylenimine (Beu et al., J. Comput. Chem ., 2020, 41, 349). With supporting evidence, we demonstrate that the new coarse‐graining methodology presented in that work is inconsistent with the Martini methodology and lacks important validation steps which is usually required by Martini forcefields. Abstract : The coarse‐graining methodology used by Beu et al. J. Comp. Chem ., 2020, 41, 349 did not follow the Martini methodology: (i) bonded parameters were not iteratively improved, (ii) nonbonded parameters depended on the quality of bonded parameters, and (iii) compatibility of coarse‐grained polyethylenimine (PEI) model with Martini DNA was not verified. The potential of mean force between PEI and DNA calculated using nonbonded parameters from Beu et al. performed notably worse than the result using nonbonded parameters obtained from Martini methodology.