MDWiZ: a platform for the automated translation of molecular dynamics simulations

AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD

All-atom molecular dynamics (MD) simulations are an essential structural biology technique with increasing application to multimillion-atom systems, including viruses and cellular machinery. Classical MD simulations rely on parameter sets, such as the AMBER family of force fields (AMBERff), to accurately describe molecular motion. Here, we present an implementation of AMBERff for use in NAMD that overcomes previous limitations to enable high-performance, massively parallel simulations encompassing up to two billion atoms. Single-point potential energy comparisons and case studies on model systems demonstrate that the implementation produces results that are as accurate as running AMBERff in its native engine.

Facilitating CG Simulations with MAD: The MArtini Database Server

The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.

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

Preparing input files for molecular dynamics (MD) simulations can be a tedious task, particularly if different MD programs need to be used. Most simulation packages are accompanied by applications that handle this task, and, in some cases, software to perform interconversion between MD programs can be found. However, the conversion between different types of files is not always foolproof or the force field may not be fully supported, as quite often observed with polarization models. This work describes the program DLPGEN, which produces input files for the MD programs GROMACS, CHARMM, DL_POLY, and LAMMPS. The program can prepare polarizable force fields using a self-consistent field approach or with a dual thermostat-extended Lagrangian model. For GROMACS, a new polarization scheme suitable for the simulation of molecules containing more than one virtual particle is described. Results obtained for ethanol in the liquid state revealed that the system configurational energy, liquid density, and self-diffusion coefficient obtained with GROMACS are in good agreement with the data found with LAMMPS and CHARMM. In the case of DL_POLY, a problem with the Shells temperature control was found, suggesting that this program may not be suitable for the simulation of molecules containing multiple Drude particles.

From GROMACS to LAMMPS: GRO2LAM : A converter for molecular dynamics software

Atomistic simulations have progressively attracted attention in the study of physical-chemical properties of innovative nanomaterials. GROMACS and LAMMPS are currently the most widespread open-source software for molecular dynamics simulations thanks to their good flexibility, numerous functionalities and responsive community support. Nevertheless, the very different formats adopted for input and output files are limiting the possibility to transfer GROMACS simulations to LAMMPS. In this article, we present GRO2LAM, a modular and open-source Python 2.7 code for rapidly translating input files and parameters from GROMACS to LAMMPS format. The robustness of the tool has been assessed by comparing the simulation results obtained by GROMACS and LAMMPS, after the format conversion by GRO2LAM. Specifically, three nanoscale configurations of interest in both engineering and biomedical fields are studied, namely a carbon nanotube, an iron oxide nanoparticle, and a protein immersed in water. In perspective, GRO2LAM may be the first step to achieve a full interoperability between molecular dynamics software. This would allow to easily exploit their complementary potentialities and post-processing functionalities. Moreover, GRO2LAM could facilitate the cross-check of simulation results, guaranteeing the reproducibility of molecular dynamics models and testing their robustness. Graphical Abstract GRO2LAM, a modular and open-source Python code for rapidly translating input files and parameters from GROMACS to LAMMPS format.

ForConX: A forcefield conversion tool based on XML

The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey-Bradley and Ryckaert-Bellemans potentials. © 2017 Wiley Periodicals, Inc.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

Using a molecular model for octamethylcyclotetrasiloxane (OMCTS), molecular dynamics simulations are carried out to probe the phase state of OMCTS confined between two mica surfaces in equilibrium with a reservoir. Molecular dynamics simulations are carried out for elevations ranging from 5 to 35 K above the melting point for the OMCTS model used in this study. The Helmholtz free energy is computed for a specific confinement using the two-phase thermodynamic (2PT) method. Analysis of the in-plane pair correlation functions did not reveal signatures of freezing even under an extreme confinement of two layers. OMCTS is found to orient with a wide distribution of orientations with respect to the mica surface, with a distinct preference for the surface parallel configuration in the contact layers. The self-intermediate scattering function is found to decay with increasing relaxation times as the surface separation is decreased, and the two-step relaxation in the scattering function, a signature of glassy dynamics, distinctly evolves as the temperature is lowered. However, even at 5 K above the melting point, we did not observe a freezing transition and the self-intermediate scattering functions relax within 200 ps for the seven-layered confined system. The self-diffusivity and relaxation times obtained from the Kohlrausch-Williams-Watts stretched exponential fits to the late α-relaxation exhibit power law scalings with the packing fraction as predicted by mode coupling theory. A distinct discontinuity in the Helmholtz free energy, potential energy, and a sharp change in the local bond order parameter, Q4, was observed at 230 K for a five-layered system upon cooling, indicative of a first-order transition. A freezing point depression of about 30 K was observed for this five-layered confined system, and at the lower temperatures, contact layers were found to be disordered with long-range order present only in the inner layers. These dynamical signatures indicate that confined OMCTS undergoes a slowdown akin to a fluid approaching a glass transition upon increasing confinement, and freezing under confinement would require substantial subcooling below the bulk melting point of OMCTS.