[Show abstract][Hide abstract] ABSTRACT: GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.
5 10/2014; Royal Institute of Technology and Uppsala University, Sweden..
[Show abstract][Hide abstract] ABSTRACT: The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters—far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.
Journal of Chemical Theory and Computation 07/2013; 9(8):3527–3537. · 5.39 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Calculating interactions or correlations between pairs of particles is
typically the most time-consuming task in particle simulation or correlation
analysis. Straightforward implementations using a double loop over particle
pairs have traditionally worked well, especially since compilers usually do a
good job of unrolling the inner loop. In order to reach high performance on
modern CPU and accelerator architectures, single-instruction multiple-data
(SIMD) parallelization has become essential. Avoiding memory bottlenecks is
also increasingly important and requires reducing the ratio of memory to
arithmetic operations. Moreover, when pairs only interact within a certain
cut-off distance, good SIMD utilization can only be achieved by reordering
input and output data, which quickly becomes a limiting factor. Here we present
an algorithm for SIMD parallelization based on grouping a fixed number of
particles, e.g. 2, 4, or 8, into spatial clusters. Calculating all interactions
between particles in a pair of such clusters improves data reuse compared to
the traditional scheme and results in a more efficient SIMD parallelization.
Adjusting the cluster size allows the algorithm to map to SIMD units of various
widths. This flexibility not only enables fast and efficient implementation on
current CPUs and accelerator architectures like GPUs or Intel MIC, but it also
makes the algorithm future-proof. We present the algorithm with an application
to molecular dynamics simulations, where we can also make use of the effective
buffering the method introduces.
[Show abstract][Hide abstract] ABSTRACT: The training event includes tutorials on basic and advanced usage of two major packages for Molecular Dynamics simulations – GROMACS and AMBER – with focus on their application to modelling of biomolecular systems. The following sessions will include the presentation of two portals for automated submission of jobs developed by the WeNMR (wenmr.eu) and ScalaLife (scalalife.eu).
[Show abstract][Hide abstract] ABSTRACT: Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: firstname.lastname@example.org Supplementary information:Supplementary data are available at Bioinformatics online.
[Show abstract][Hide abstract] ABSTRACT: MOTIVATION: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. RESULTS: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. AVAILABILITY: GROMACS is an open source and free software available from http://www.gromacs.org. CONTACT: email@example.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
[Show abstract][Hide abstract] ABSTRACT: Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations.
Chemistry and Physics of Lipids 01/2013; · 2.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The gating of voltage-gated ion channels is controlled by the arginine-rich S4 helix of the voltage-sensor domain moving in response to an external potential. Recent studies have suggested that S4 moves in three to four steps to open the conducting pore, thus visiting several intermediate conformations during gating. However, the exact conformational changes are not known in detail. For instance, it has been suggested that there is a local rotation in the helix corresponding to short segments of a 3[Formula: see text]-helix moving along S4 during opening and closing. Here, we have explored the energetics of the transition between the fully open state (based on the X-ray structure) and the first intermediate state towards channel closing (C[Formula: see text]), modeled from experimental constraints. We show that conformations within 3 Å of the X-ray structure are obtained in simulations starting from the C[Formula: see text] model, and directly observe the previously suggested sliding 3[Formula: see text]-helix region in S4. Through systematic free energy calculations, we show that the C[Formula: see text] state is a stable intermediate conformation and determine free energy profiles for moving between the states without constraints. Mutations indicate several residues in a narrow hydrophobic band in the voltage sensor contribute to the barrier between the open and C[Formula: see text] states, with F233 in the S2 helix having the largest influence. Substitution for smaller amino acids reduces the transition cost, while introduction of a larger ring increases it, largely confirming experimental activation shift results. There is a systematic correlation between the local aromatic ring rotation, the arginine barrier crossing, and the corresponding relative free energy. In particular, it appears to be more advantageous for the F233 side chain to rotate towards the extracellular side when arginines cross the hydrophobic region.
PLoS ONE 01/2012; 7(10):e45880. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models propose combinations of translation, rotation, and tilt to reach the resting state. Recently, experiments and simulations have independently observed occurrence of 3(10)-helix in S4. This suggests S4 might make a transition from α- to 3(10)-helix in the gating process. Here, we show 3(10)-helix structure between Q1 and R3 in the S4 segment of a voltage sensor appears to facilitate the early stage of the motion toward a down state. We use multiple microsecond-steered molecular simulations to calculate the work required for translating S4 both as α-helix and transformed to 3(10)-helix. The barrier appears to be caused by salt-bridge reformation simultaneous to R4 passing the F233 hydrophobic lock, and it is almost a factor-two lower with 3(10)-helix. The latter facilitates translation because R2/R3 line up to face E183/E226, which reduces the requirement to rotate S4. This is also reflected in a lower root mean-square deviation distortion of the rest of the voltage sensor. This supports the 3(10) hypothesis, and could explain some of the differences between the open-inactivated- versus activated-states.
[Show abstract][Hide abstract] ABSTRACT: Several GPU-based algorithms have been developed to accelerate biomolecular simulations, but although they provide benefits over single-core implementations, they have not been able to surpass the performance of state-of-the art SIMD CPU implementations (e.g. GROMACS), not to mention efficient scaling. Here, we present a heterogenous parallelization that utilizes both CPU and GPU resources efficiently. A novel fixed-particle-number sub-cell algorithm for non-bonded force calculation was developed. The algorithm uses the SIMD width as algorithmic work unit, it is intrinsically future-proof since it can be adapted to future hardware. The CUDA non-bonded kernel implementation achieves up to 60\% work-efficiency, 1.5 IPC, and 95\% L1 cache utilization. On the CPU OpenMP-parallelized SSE-accelerated code runs overlapping with GPU execution. Fully automated dynamic inter-process as well as CPU-GPU load balancing is employed. We achieve threefold speedup compared to equivalent GROMACS CPU code and show good strong and weak scaling. To the best of our knowledge this the fastest GPU molecular dynamics implementation presented to date.
Conference on High Performance Computing Networking, Storage and Analysis - Companion Volume, SC 2011, Seattle, WA, USA, November 12-18, 2011; 01/2011
[Show abstract][Hide abstract] ABSTRACT: Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring. Copernicus enables execution as single parallel jobs with automatic resource allocation. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. Starting from extended chains we observe structures 0.6 Å from the native state within 30h, and achieve sufficient sampling to predict the native state without a priori knowledge after 80--90h. To match Copernicus' efficiency, a classical simulation would have to exceed 50 microseconds per day, currently infeasible even with custom hardware designed for simulations.
Conference on High Performance Computing Networking, Storage and Analysis, SC 2011, Seattle, WA, USA, November 12-18, 2011; 01/2011
[Show abstract][Hide abstract] ABSTRACT: We have studied the partitioning of amphiphilic peptides at the air-water interface. The free energy of adsorption from bulk to interface was calculated by determining the potential of mean force via atomistic molecular dynamics simulations. To this end a method is introduced to restrain or constrain the center of mass of a group of molecules in a periodic system. The model amphiphilic peptides are composed of alternating valine and asparagine residues. The decomposition of the free energy difference between the bulk and interface is studied for different peptide block lengths. Our analysis revealed that for short amphiphilic peptides the surface driving force dominantly stems from the dehydration of hydrophobic side chains. The only opposing force is associated with the loss of orientational freedom of the peptide at the interface. For the peptides studied, the free energy difference scales linearly with the size of the molecule, since the peptides mainly adopt extended conformations both in bulk and at the interface. The free energy difference depends strongly on the water model, which can be rationalized through the hydration thermodynamics of hydrophobic solutes. Finally, we measured the reduction of the surface tension associated with complete coverage of the interface with peptides.
The Journal of Physical Chemistry B 09/2010; 114(34):11093-101. · 3.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the , ψ protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.
Journal of Chemical Theory and Computation - J CHEM THEORY COMPUT. 01/2010; 6(2).
[Show abstract][Hide abstract] ABSTRACT: Aqueous solutions of a light (Nd3+), a middle (Gd3+), and a heavy (Yb3+) lanthanide ion were studied using ab initio based flexible and polarizable analytical potentials in classical molecular dynamics simulations to describe their thermodynamic, structural, and dynamic features. To avoid the spurious demise of O-H bonds, it was necessary to reparametrize an existing water model, which resulted in an improved description of pure water. The good agreement of the results from the simulations with the experimental hydration enthalpies, the Ln(III)-water radial distribution functions, and the water-exchange rates validated the potentials, though the r(Ln-Ow) distances were 6% longer than the experimentally determined values. A nona-coordinated state was found for Nd3+ in 95% of the simulation, with a tricapped trigonal prism (TCTP) geometry; the corresponding water-exchange mechanism was found to be of dissociative interchange (Id) character through a short-lived octa-coordinated transition state in a square antiprism (SQA) geometry. An octa-coordinated state in SQA geometry was found for Yb3+ in 99% of the simulation, and the observed exchange events exhibited characteristics of an interchange (I) mechanism. For Gd3+ an equilibrium was observed between 8-fold SQA and 9-fold TCTP coordinated states that was maintained by the frequent exchange of a water molecule from the first hydration shell with the bulk, thus producing significant deviations from the ideal geometries, and a fast exchange rate. Though strong water-water interactions prevented a full alignment of the dipoles to the ion's electric field, the screening was found large enough as to limit its range to 5 A; water molecules further apart from the ion were found to have the same dipole as the molecules in the bulk, and a random orientation. The interplay among the water-ion and the water-water interactions determined the different coordination numbers and the different dynamics of the water exchange in the first hydration shell for each ion.
The Journal of Physical Chemistry B 05/2009; 113(20):7270-81. · 3.61 Impact Factor