Gramm-software package for molecular dynamics on graphical processing units

Tetracycline (TC) and its derivatives have recently been proposed as a new class of antagonists in prion diseases as they prevent the aggregation of prion protein peptides and their acquisition of protease resistance in vitro and in vivo. Looking for relationships between conformational flexibility and biological activity, we searched for a geometrical pharmacophore by investigating, in aqueous solution, the conformational behavior of 15 TCs in both the zwitterionic and the anionic forms. For TC similar conformational flexibility was found for the two forms and two main conformational families were detected, an extended and a folded conformation characterized by different intramolecular hydrogen-bond networks. On comparing the Molecular Mechanics results with the ab initio ones and the experimental evidence, it can be seen that the conformational behavior of TC is reasonably well predicted by the MM2 force field, whereas the conformational energies provided by the Amber force field are unreliable. The conformational analysis of the other TC derivatives was then performed by the MM2 force field. As a result, their conformational behavior was similar to that observed for TC itself. Despite the hydronaphthacene moiety's conformational flexibility, no geometrical pharmacophore was found among the TCs, i.e. properties other than geometrical ones should play a crucial role in determining their anti-fibrillogenic ability.

ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol's sequential performance is excellent when compared to a leading MD program, and that it scales well for moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.

Discrete approaches for the nonlinear analysis of in plane loaded masonry walls: Molecular dynamic and static algorithm solutions

Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics

13C NMR spectroscopy, ab initio quantum mechanics, and molecular mechanics have been used to investigate the trans-4-(trifluoromethyl)-2,2,6-trimethyl-1,3-dioxane chair/twist-boat equilibrium. The molecular mechanics calculations were based upon the MM3 and AMBER force fields. A 6-31G basis set was used for the ab initio calculations, and MP2 correlation corrections were applied. Both the ab initio and AMBER molecular mechanics calculations are consistent with the (13)C NMR chemical shift differences for the trans-4-(trifluoromethyl)-2,2,6-trimethyl-1,3-dioxane conformers. The predicted chair to twist-boat equilibrium suggested by the MM3 calculations is not consistent with the experimental data. These results support the suggestion by Howard et al. (Howard, A. E.; Cieplak, P.; Kollman, P. A. J. Comput.Chem. 1995, 16, 243-261) on the critical role of electrostatic interactions in determining the chair/twist-boat equilibrium.

MM3 force field as a tool in mechanistic studies of nitrogen inversion processes for alkylamines

Molecular mechanics (MM3) calculations on phosphonamidate compounds

We compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and the solvent is represented by either one of the well-known SPC and TIP3P models. All MM force fields give two main states for Ace-Ala-Nme, beta and alpha separated by free energy barriers, but the ratio in which these are sampled varies by a factor of 30, from a high in favor of beta of 6 to a low of 1/5. The frequency of transitions between states is particularly low with the amber and charmm force fields, for which the distributions are noticeably narrower, and the energy barriers between states higher. The lower of the two barriers lies between alpha and beta at values of psi near 0 for all MM simulations except for charmm22. The results of the QM/MM simulations vary less with the choice of MM force field; the ratio beta/alpha varies between 1.5 and 2.2, the easy pass lies at psi near 0, and transitions between states are more frequent than for amber and charmm, but less frequent than for cedar. For Ace-Gly-Nme, all force fields locate a diffuse stable region around phi = pi and psi = pi, whereas the amber force field gives two additional densely sampled states near phi = +/-100 degrees and psi = 0, which are also found with the QM/MM force field. For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in high-resolution protein structures than is the case for any of the MM simulations.

Conformational analysis of crown ethers—part 2. 15-crown-5

The structures of cyclic oligomers of glucopyranose, small size, theoretical cyclic oligomers up to the γ-cyclodextrin have been optimized by AMI and PM3 semiempirical (SE) methods, and MM2, AMBER, and CHARMM Molecular Mechanics (MM) force fields. Ab initio optimization for glucose was also done at STO-3G level. In order to study the differences in the heat of formations of the various optimized geometries more detailed calculations were performed on the various CH2OH rotamers of glucose.

Molecular dynamics (MD) simulation in the explicit water is performed to study the interaction mechanism of trypsin-ligand binding under the AMBER force field and polarized protein-specific charge (PPC) force field combined the new developed highly efficient interaction entropy (IE) method for calculation of entropy change. And the detailed analysis and comparison of the results of MD simulation for two trypsin-ligand systems show that the root-mean-square deviation (RMSD) of backbone atoms, B-factor, intra-protein and protein-ligand hydrogen bonds are more stable under PPC force field than AMBER force field. Our results demonstrate that the IE method is superior than the traditional normal mode (Nmode) method in the calculation of entropy change and the calculated binding free energy under the PPC force field combined with the IE method is more close to the experimental value than other three combinations (AMBER-Nmode, AMBER-IE and PPC-Nmode). And three critical hydrogen bonds between trypsin and ligand are broken under AMBER force field. However, they are well preserved under PPC force field. Detailed binding interactions of ligands with trypsin are further analyzed. The present work demonstrates that the polarized force field combined the highly efficient IE method is critical in MD simulation and free energy calculation.

The lone-pair…π (lp…π) (deoxy)ribose…nucleobase stacking is a recurring structural motif in Z DNA and RNAs that is characterized by sub-van der Waals lp…π contacts (<3.0 Å). It is part of the structural signature of the CpG Z-steps in Z-DNA and r(UNCG) tetraloops. These nucleic acid structures are poorly behaving in molecular dynamics (MD) simulations. Although the exact origin of these issues remains unclear, a significant part of the problem might be due to an imbalanced description of non-bonded interactions including the characteristic lp…π stacking. To gain insights into the links between lp…π stacking and MD issues, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the non-bonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, U). Among other differences, we found that the AFF overestimates the DHDF D3 lp…π distances by ~0.1-0.2 Å while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule (AIM) polarizabilities and SAPT analysis, we inferred that the DHDF-D3 vs. AFF differences partly originate in the Lennard-Jones (LJ) parameters that are identical for nucleobase carbon atoms despite the presence/absence of connected electron withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp…π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.

We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.

ABSTRACTWe introduce a Discard-and-Restart molecular dynamics (MD) algorithm tailored for the sampling of realistic protein transition states. It aids computational structure-based drug discovery by reducing the simulation times to compute transition pathways by up to 2000x. The algorithm iteratively performs short MD simulations and measures their proximity to a target state via a collective variable (CV) loss, which can be defined in a flexible fashion, locally or globally. Using the loss, if the trajectory proceeds toward the target, the MD simulation continues. Otherwise, it is discarded and a new MD simulation is restarted, with new initial velocities randomly drawn from a Boltzmann distribution. The discard-and-restart algorithm demonstrates efficacy and atomistic accuracy in capturing the folding pathways in several contexts: (1) fast-folding small protein domains; (2) the folding intermediate of the prion protein PrP; and (3) the spontaneous partial unfolding of α-Tubulin, a crucial event for microtubule severing. During each iteration of the algorithm, we are able to perform AI-based analysis of the transitory conformations to find binding pockets, which could potentially represent druggable sites. Overall, our algorithm enables systematic and computationally efficient exploration of conformational landscapes, enhancing the design of ligands targeting dynamic protein states.

A discard-and-restart MD algorithm for the sampling of protein intermediate states.