DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields

CES Bernardes, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 62, 1471-1478 (2022).

DOI: 10.1021/acs.jcim.1c01431

Preparing inputfiles for molecular dynamics (MD)simulations can be a tedious task, particularly if different MDprograms need to be used. Most simulation packages areaccompanied by applications that handle this task, and, in somecases, software to perform interconversion between MD programscan be found. However, the conversion between different types offiles is not always foolproof or the forcefield may not be fullysupported, as quite often observed with polarization models. Thiswork describes the program DLPGEN, which produces inputfilesfor the MD programs GROMACS, CHARMM, DL_POLY, andLAMMPS. The program can prepare polarizable forcefields using a self-consistentfield approach or with a dual thermostat-extendedLagrangian model. For GROMACS, a new polarization scheme suitable for the simulation of molecules containing more than onevirtual particle is described. Results obtained for ethanol in the liquid state revealed that the system configurational energy, liquiddensity, and self-diffusion coefficient obtained with GROMACS are in good agreement with the data found with LAMMPS andCHARMM. In the case of DL_POLY, a problem with the Shells temperature control was found, suggesting that this program maynot be suitable for the simulation of molecules containing multiple Drude particles

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