Self-assembling dipeptides : including solvent degrees of freedom in a coarse-grained model
2009, Villa, Alessandra, van der Vegt, Nico F. A., Peter, Christine
In the previous paper [A. Villa, C. Peter, N. F. A. van der Vegt, Phys. Chem. Chem. Phys., 2009, DOI: ], a strategy to develop a solvent-free coarse-grained model for peptides is outlined which is based on an atomistic (force field) description. The coarse-grained model is designed such that it correctly captures the conformational flexibility of the molecules and reproduces the interaction between peptides in aqueous solution. In the present paper, we revisit this model and present a method to devise nonbonded interactions such that also the coarse-grained level maintains explicit solvent degrees of freedom. In this new approach we rely on a structure-based coarse graining methodology which preserves the solvation structure around the peptides in combination with a method to devise nonbonded potentials between peptide beads in a way that the peptide-peptide interaction in water is represented correctly and that results in the correct thermodynamic association behavior. The outlined coarse graining strategy provides us with two (one implicit- and one explicit-solvent) models that are well suited for multiscale-simulation and scale-bridging purposes. We show that this is a powerful tool to efficiently simulate long time-scale and large length-scale biomolecular processes such as peptide self-assembly. In combination with an efficient backmapping methodology we can obtain well-equilibrated atomistic structures of the resulting aggregates.
Fast-Growth Thermodynamic Integration : Calculating Excess Chemical Potentials of Additive Molecules in Polymer Microstructures
2008, Hess, Berk, Peter, Christine, Ozal, Tugba, van der Vegt, Nico F. A.
We have calculated excess chemical potentials of additive molecules in a bisphenol A-polycarbonate matrix using fast-growth thermodynamic integration. It is shown that this method, which is based on Jarzynski's nonequilibrium work theorem, is ideally suited to overcome some of the typical sampling problems one meets when inserting large additive molecules into a dense polymer matrix. The method provides a direct link between the calculated excess chemical potential and the atomic-scale environment preferred by the inserted molecule. We discuss for which types of free-energy landscapes fast-growth thermodynamic integration is well suited and which are the optimal parameters to use.
The GROMOS software for biomolecular simulation : GROMOS05
2005-12, Christen, Markus, Hünenberger, Philippe H., Bakowies, Dirk, Baron, Riccardo, Bürgi, Roland, Geerke, Daan P., Heinz, Tim N., Kastenholz, Mika A., Kräutler, Vincent, Oostenbrink, Chris, Peter, Christine, Trzesniak, Daniel, van Gunsteren, Wilfred F.
We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented.
Multiscale simulation of soft matter systems : from the atomistic to the coarse-grained level and back
2009, Peter, Christine, Kremer, Kurt
Many physical phenomena and properties of soft matter systems such as synthetic or biological materials are governed by interactions and processes on a wide range of length- and time-scales. Computer simulation approaches that are targeted at questions in these systems require models which cover these scales and the respective levels of resolution. Multiscale simulation methods combine and systematically link several simulation hierarchies so that they can address phenomena at multiple levels of resolution. In order to reach the mesoscopic time- and length-scales important for many material properties, methods that bridge from the atomistic (microscopic) to a coarser (mesocopic) level are developed. Here, we review coarse-grained simulation models that are linked to a higher resolution atomistic description. In particular, we focus on structure-based coarse-graining methods which are used for a variety of soft matter problems – ranging from structure-formation in amorphous polymers to biomolecular aggregation. It is shown that by coarse-grained simulation in combination with an efficient backmapping methodology one can obtain well-equilibrated long time- and large length-scale atomistic structures of polymeric melts or biomolecular aggregates which can be used for comparison to experimental data. Methodological aspects are addressed such as the question of the time-scales and dynamics in the different simulation hierarchies and an outlook to future challenges in the area of resolution exchange approaches and adaptive resolution models is presented.
Modeling Solubilities of Additives in Polymer Microstructures : Single-Step Perturbation Method Based on a Soft-Cavity Reference State
2008-07, Özal, Tugba A., Peter, Christine, Hess, Berk, van der Vegt, Nico F. A.
Solubilities of additive molecules whose molecular sizes exceed the typical dimensions of free volume cavities pre-existing in amorphous polymer melts and glasses cannot readily be computed in molecular simulations. In this paper, we perform molecular dynamics simulations of a soft-cavity reference state ensemble, which contains a soft-core, fast diffusing, Lennard-Jones particle in a rigid-chain polymer matrix. By means of the Zwanzig thermodynamic perturbation formalism, the soft particle has been perturbed to various real-solute end-states. It is shown that with this approach it is possible to overcome some of the free energy sampling problems related to the insertion of large solutes and slow diffusion in the end-state. We have calculated the excess chemical potentials of propane, chloroform, and dimethyl sulfoxide in liquid bisphenol A−polycarbonate and show that a single simulation of the reference state is sufficient to obtain statistical accuracies within error bars of 0.5−0.8 kBT. The method is particularly useful for calculating solubility ratios of large molecular solutes with approximately equal excluded volume radii.
Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals
2007-09, Böckmann, Marcus, Peter, Christine, Delle Site, Luigi, Doltsinis, Nikos L., Kremer, Kurt, Marx, Dominik
An atomistic force field has been adapted for use in molecular dynamics simulations of molecular materials that contain azobenzene (AB) functional groups. Force field parameters for bonded interactions and partial charges in the AB unit have been derived from ab initio molecular dynamics reference calculations. First applications of the new force field to liquid trans- and cis-AB are presented, both using a purely classical approach (MM) and a hybrid quantum-classical (QM/MM) simulation scheme. Detailed structural analysis confirms that QM/MM and purely MM simulations yield results that are in good agreement with each other. The force field of the AB core has been extended to include aliphatic chains that are attached via ether bridges to the two AB benzene rings. This allows for studying temperature induced phase transitions in the liquid-crystalline 8AB8 system. Using replica exchange techniques the new force field has successfully reproduced the smectic to isotropic-phase transition.
Self-assembling dipeptides : conformational sampling in solvent-free coarse-grained simulation
2009, Villa, Alessandra, Peter, Christine, van der Vegt, Nico F. A.
We discuss the development of a coarse-grained (CG) model for molecular dynamics (MD) simulation of a hydrophobic dipeptide, diphenylalanine, in aqueous solution. The peptide backbone is described with two CG beads per amino acid, the side groups and charged end groups are each described with one CG bead. In the derivation of interaction functions between CG beads we follow a bottom-up strategy where we devise potentials such that the resulting CG simulation reproduces the conformational sampling and the intermolecular interactions observed in an atomistic simulation of the same peptide. In the CG model, conformational flexibility of the peptide is accounted for through a set of intra-molecular (bonded) potentials. The approach followed to obtain the bonded potentials is discussed in detail. The CG potentials for nonbonded interactions are based on potentials of mean force obtained by atomistic simulations in aqueous solution. Following this approach, solvent mediation effects are included in the effective bead-bead nonbonded interactions and computationally very efficient (solvent-free) simulations of self-assembly processes can be performed. We show that the conformational properties of the all-atom dipeptide in explicit solvent can be accurately reproduced with the CG model. Moreover, preliminary simulations of peptide self-assembly performed with the CG model illustrate good agreement with results obtained from all-atom, explicit solvent simulations.
Classical simulations from the atomistic to the mesoscale and back : coarse graining an azobenzene liquid crystal
2008, Peter, Christine, Delle Site, Luigi, Kremer, Kurt
We describe the development of a coarse grained model for molecular dynamics (MD) simulations of a liquid-crystalline (LC) compound with an azobenzene mesogen. It is investigated how coarse graining methods originally developed to simulate amorphous polymeric systems can be extended to liquid crystals. The coarse grained (CG) model is constructed in a way that it allows carrying over of chemical details (i.e. the form of specific/attractive interactions) from the atomistic to the CG level, devising a new route to construct mesoscale models for liquid crystals with a close link to chemically more realistic atomistic ones. In addition it is possible to switch between the atomistic and the CG levels of resolution on demand through an inverse mapping procedure. By this we obtain representative large-scale atomistic coordinates based on CG structures and long-time atomistic trajectories generated from CG mesoscale simulations.
Solvent Reorganization Contributions in Solute Transfer Thermodynamics : Inferences from the Solvent Equation of State
2007, Peter, Christine, van der Vegt, Nico F. A.
Solvation enthalpies of simple solutes contain contributions from (1) solute-solvent interactions and (2) solute-induced modifications of solvent-solvent interactions (solvent reorganization). It has recently been suggested in the literature that these contributions can, under certain conditions, be estimated with additional experimental data on thermodynamic response functions of the pure solvent (coefficient of thermal expansion, isothermal compressibility) and the solute solvation volume. We analyze and discuss these conditions based on computer simulations of a series of polar and nonpolar solutes in a polar and nonpolar liquid solvent.