Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding ...
a non-specific force field variant was also prepared. The values of allεparameters, governing the interaction strength between two given pseudoatoms, were equalized to an averageεvalue from the full protein-DNA force field. At the same time,σparameters...
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interac
PolySMart is a python package which is designed to perform a reactive MD simulation in GROMACS MD package using MARTINI coarse-grain forcefield. It is specially designed to perform polymerization and crosslinking process in order to generate the topology of the resulting structure at any stage of...
The Martini coarse-grained force field.A Coarse Grain Model for Phospholipid SimulationsCoarse-grained normal mode analysis in structural biologyCoarse-to-fine n -best parsing and MaxEnt discriminative rerankingA method of sampling coarse river‐bed materialA method of sampling coarse river‐bed ...
The Martini coarse-grained force field. A Coarse Grain Model for Phospholipid Simulations Coarse-grained normal mode analysis in structural biology Coarse-to-fine n -best parsing and MaxEnt discriminative reranking A method of sampling coarse river‐bed material ...
coarse-grainforce matchingfluctuation matchingbiological membranelipid bilayerTwo new approaches are presented for obtaining coarse-grained (CG) force fields from atomistic molecular dynamics (MD) trajectories. The first approach is the force-matching (FM) method whereby the force data obtained from an ...
Knotts T IV, Rathore N, Schwartz DC, de Pablo JJ (2007) A coarse grain model for DNA. J Chem Phys 126:084901 Google Scholar Voltz K, Trylska J, Tozzini V, Kurkal-Siebert V, Langowski J, Smith J (2008) Coarse-grained force field for the nucleosome from self-consistent multiscaling...
There are no widely accepted approaches to coarse-grain modeling. The specific methods used depend on the materials system and the conditions under which the materials are simulated. Some general overviews of coarse-graining can be found elsewhere.31,32 Several research groups have developed methods ...
a non-specific force field variant was also prepared. The values of allεparameters, governing the interaction strength between two given pseudoatoms, were equalized to an averageεvalue from the full protein-DNA force field. At the same time,σparameters...