We present software package MagiC, which is designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modeling of the system in a high resolution (atomistic) description. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated nonbonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the latter accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, allowing parallel simulation of many copies of the system with subsequent averaging of the properties, which provides fast convergence of the method with nearly linear scaling at parallel execution.
Accurate parametrization of force fields (FFs) is of
ultimate importance
for computer simulations to be reliable and to possess a predictive
power. In this work, we analyzed, in multi-microsecond simulations
of a 40-base-pair DNA fragment, the performance of four force fields,
namely, the two recent major updates of CHARMM and two from the AMBER
family. We focused on a description of double-helix DNA flexibility
and dynamics both at atomistic and at mesoscale level in coarse-grained
(CG) simulations. In addition to the traditional analysis of different
base-pair and base-step parameters, we extended our analysis to investigate
the ability of the force field to parametrize a CG DNA model by structure-based
bottom-up coarse-graining, computing DNA persistence length as a function
of ionic strength. Our simulations unambiguously showed that the CHARMM36
force field is unable to preserve DNA’s structural stability
at over-microsecond time scale. Both versions of the AMBER FF, parmbsc0
and parmbsc1, showed good agreement with experiment, with some bias
of parmbsc0 parameters for intermediate A/B form DNA structures. The
CHARMM27 force field provides stable atomistic trajectories and overall
(among the considered force fields) the best fit to experimentally
determined DNA flexibility parameters both at atomistic and at mesoscale
level.
The effective solvent-mediated potentials for Na + and Cl À ions in aqueous solution were calculated in a wide range of temperatures from 0 to 100 1C. The potentials have been determined using the inverse Monte Carlo approach, from the ion-ion radial distribution functions computed in 50 ns molecular dynamics simulations of ions and explicit water molecules. We further separated the effective potentials into a short-range part and an electrostatic long-range part represented by a coulombic potential with some dielectric permittivity. We adjusted the value of the dielectric permittivity to provide the fastest possible decay of the short-range potentials at larger distances. The obtained temperature dependence of the dielectric permittivity follows well the experimental data. We show also that the largest part of the temperature dependence of the effective potentials can be attributed to the temperature-dependent dielectric permittivity.
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