Relevant bibliographies by topics / GROMACS

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'GROMACS'

Author: Grafiati
Published: 4 June 2021
Last updated: 11 March 2023

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Journal articles on the topic "GROMACS"

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Irrgang, M. Eric, Caroline Davis, and Peter M. Kasson. "gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support." PLOS Computational Biology 18, no. 2 (February 14, 2022): e1009835. http://dx.doi.org/10.1371/journal.pcbi.1009835.

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Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.
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van der Spoel, David, and Berk Hess. "GROMACS—the road ahead." WIREs Computational Molecular Science 1, no. 5 (April 25, 2011): 710–15. http://dx.doi.org/10.1002/wcms.50.

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Briones, Rodolfo, Christian Blau, Carsten Kutzner, Bert L. de Groot, and Camilo Aponte-Santamaría. "GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations." Biophysical Journal 116, no. 1 (January 2019): 4–11. http://dx.doi.org/10.1016/j.bpj.2018.11.3126.

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Briones, Rodolfo, Christian Blau, Carsten Kutzner, Bert L. de Groot, and Camilo Aponte-Santamaría. "Gromaps: A Gromacs-Based Toolset to Analyse Density Maps Derived from Molecular Dynamics Simulations." Biophysical Journal 116, no. 3 (February 2019): 142a—143a. http://dx.doi.org/10.1016/j.bpj.2018.11.790.

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van der Spoel, D., P. J. van Maaren, and C. Caleman. "GROMACS molecule & liquid database." Bioinformatics 28, no. 5 (January 11, 2012): 752–53. http://dx.doi.org/10.1093/bioinformatics/bts020.

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Nava, M. "Implementing dimer metadynamics using gromacs." Journal of Computational Chemistry 39, no. 25 (September 30, 2018): 2126–32. http://dx.doi.org/10.1002/jcc.25386.

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Van Der Spoel, David, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, and Herman J. C. Berendsen. "GROMACS: Fast, flexible, and free." Journal of Computational Chemistry 26, no. 16 (2005): 1701–18. http://dx.doi.org/10.1002/jcc.20291.

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Nguyen, Trang Truc, Man Hoang Viet, and Mai Suan Li. "Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase." Scientific World Journal 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/536084.

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The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energyΔGbindof oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus.ΔGbindis estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fieldsΔGbinddecays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.
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Sellis, Diamantis, Dimitrios Vlachakis, and Metaxia Vlassi. "Gromita: A Fully Integrated Graphical user Interface to Gromacs 4." Bioinformatics and Biology Insights 3 (January 2009): BBI.S3207. http://dx.doi.org/10.4137/bbi.s3207.

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Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/ .
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Hyun, Haelee, Do Heon Kim, and Young-Ouk Lee. "Validation of Thermal Neutron Scattering Cross Sections for Heavy Water based on Molecular Dynamics Simulation." EPJ Web of Conferences 211 (2019): 06001. http://dx.doi.org/10.1051/epjconf/201921106001.

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Recently, the thermal scattering libraries of ENDF/B-VIII.0 and JEFF-3.3 for light and heavy water were released with a new water model (CAB model) proposed by Damian. For the CAB model, the molecular dynamics code GROMACS was used to more accurately describe the realistic motions of water molecules. In this paper, to consider the coherent component we also generated the thermal scattering cross section of the deuterium and oxygen bound in the heavy water molecules using the GROMACS code and EPSR code. In addition, the frequency spectrum was also calculated using the GROMACS code. Thermal scattering cross sections based on the newly calculated Sköld correction factor and the frequency spectrum were generated by NJOY2016 code. Finally, the performance of the generated thermal scattering cross sections were validated by performing an ICSBEP benchmark simulation using MCNPX code.
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Dissertations / Theses on the topic "GROMACS"

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Schwing, Gregory John. "Implementation of Replica Exchange with Dynamic Scaling in GROMACS 2018." ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/honors_theses/117.

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This is a problem of sampling. The number of classical states of an N-body system grows with O( 3 ^ N ). To sample this space, advanced techniques are required. Replica Exchange (RE), also known as parallel tempering, is an example that uses parallelization, and Hamiltonian Replica Exchange is a subset of RE that scales the energy of the replicas. The number of simulations required grows at O( N^(1/2) ), where N is number of atoms in the system. Replica Exchange with Dynamical Scaling (REDS) attempts to address this problem to decrease computational cost. It has been shown to increase efficiency 10-fold. We implemented REDS in GROMACS 2018. (Abraham 2015) All changes to the source code were written in the form of parallel methods. Scripts were written in Python and Perl to automate the experiment entirely. An exchange connects a region of high energy space, far above the surface of the landscape, to low energy space, which approaches the surface of the landscape, which represents the natural conformational progression of the molecule. Using REDS we were able to achieve exchanges at temperatures spaced too far apart to exchange using normal RE. Ergo, the flexibility of dynamical scaling allowed regions of phase space that would have gone unsampled to be mapped, addressing our initial problem of sampling.
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TRINDADE, L. C. "Simulação computacional do efeito da pressão sobre a enzima pectina metilesterase do tomate." Universidade Federal do Espírito Santo, 2018. http://repositorio.ufes.br/handle/10/7374.

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Made available in DSpace on 2018-08-01T21:59:25Z (GMT). No. of bitstreams: 1 tese_11961_Dissertação Lucas Carvalho Trindade - PPGFis (2).pdf: 9990680 bytes, checksum: a02add814af0828b765718f180e67605 (MD5) Previous issue date: 2018-02-23
Este trabalho descreve o desenvolvimento de uma simulação computacional, desenvolvida através do programa GROMACS. Mais especificamente, estudamos os resultados da simulação computacional referente a evolução do raio de giro da proteína Pectina Metilesterase (PME) do tomate em função da pressão aplicada, mantendo a temperatura fixa. Foi realizada uma descrição sobre os modelos físicos utilizados pelo programa. Também foi descrito, de forma suscinta, características sobre sistemas e estruturas dos aminoácidos e proteínas. As simulações computacionais consideraram uma temperatura de 26, 85oC e pressões aplicadas de 1 bar, 1 kbar, 3 kbar, 5 kbar, 7 kbar, 9 kbar e 10 kbar. As simulações trabalharam com um tempo de ação da pressão de até 100 pico segundos. Os resultados da simulação computacional indicaram uma redução não linear do raio de giro da enzima Pectina Metilesterase (PME) do tomate de acordo com o aumento da pressão aplicada, mantendo temperatura fixa.
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Anton, Nygren. "Experimental and theoretical studies of water droplet surfaces in the presence of glycerol." Thesis, Uppsala universitet, Institutionen för fysik och astronomi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-330979.

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Water aerosols affect the climate because they have an impact on the radiation balance and cloud formation. Water is present in all forms in the atmosphere (water, ice and steam), for example as rain and hail. Water aerosols play an important role in many biological and chemical processes in the atmosphere. The most common form of water in the atmosphere is water droplets or vapor which often come from oceans and lakes and these aerosols often contain organic compounds. It is therefore interesting to study if organic compounds, in this case glycerol, will reside on the surface or inside the water droplets. The investigations were performed by using theoretical studies, molecular dynamic simulations in GROMACS, and experimental investigations; X-ray photoelectron spectroscopy with a liquid jet. The experiments were performed at BESSY II, Berlin. The concentrations of glycerol were varied from 75:1; 8:1 to 4:1 (water: glycerol molecules). The results were that the experiments and simulations indicated that when theconcentration of glycerol increased the glycerol concentration at the surface of the waterdroplet increases until a monolayer of glycerol molecules was formed at the surface. When the monolayer was formed (or close to) less and less glycerol molecules were placed at thewater surface and more and more glycerol molecules were placed in the bulk of the waterdroplet.
Vattenaerosoler påverkar klimatet eftersom de har en inverkan på strålningsbalansen och molnbildningen. Vatten finns i alla former i atmosfären (vatten, is och ånga) som bland annat regn och hagel. Vatten aerosolerna spelar en viktig roll i många kemiska och biologiska processer i atmosfären. Den vanligaste formen av vatten i atmosfären är små vattendroppar eller ånga som ofta kommer från hav och sjöar och som ofta innehar organiska föreningar. Då vattenaerosoler påverkar klimatet och organiska föreningar är vanligt förekommande i vattendroppar är det intressant att undersöka om organiska föreningar, i detta fall glycerol, hamnar på ytan eller inuti vattnet. Undersökningarna har gjorts genom att använda teoretiska perspektiv, molekylärdynamiska simuleringar i GROMACS, samt experimentella undersökningar i form av röntgen fotoelektronspektroskopi med en vätskejet. Dessa experiment utfördes i BESSY II, Berlin. Koncentrationerna av glycerol varierades från75:1; 8:1 till 4:1 (vatten: glycerolmolekyler). Resultaten från experimenten och simuleringarna indikerade att när koncentrationen av glycerol ökade så ökade glycerolkoncentrationen på ytan av vattendroppen tills det bildades ett monolager av glycerolmolekyler på vattenytan. När monolagret hade bildats så placerades mindre och mindre glycerolmolekyler på vattenytan och fler och fler glycerolmolekyler placerades inne i vattendroppen.
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Lansing, Eric, Jennie Lodén, and Jonathan Ström. "Datorsimuleringar av modifierade cellulosafibriler." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-173482.

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The purpose of this study is to observe what modifying the surface of cellulose nanofibrils may imply for their interactions with a surrounding saline aqueous solution. This will be studied by using GROMACS, a molecular dynamic simulation software. In particular, we will analyse the modified surfaces hydrophilicity compared to native nanocellulose. This will subsequently have an impact on the nanofibrils readiness to aggregate to one another and disperse in the solution. Specifically two types of surface modifications will be studied, sulfonation and carboxy- lation. The hydrophilicity of the surfaces will be determined by analysing the density profiles of the systems wherein the modified surfaces interacts with the aqueous solutions. Also, the energies from the interactions of the simulated systems will be studied. We concluded that both modifications increases the surfaces interactions with the sur- rounding solution. Modifying the surface of the cellulose nanofibril with sulfonate will increase the surfaces attraction towards water and may provide the best rate of dispersion in aqueous solutions and best prohibit aggregation. Carboxylation of the surface provides similar hydrophilic results as the sulfonation but not as prevalent.
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Abrikossov, Alexei. "Computer simulations : Orientation of Lysozyme in vacuum under the influence of an electric field." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-151484.

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The possibility to orient a protein in space using an external electrical field was studied bymeans of molecular dynamics simulations. To model the possible conditions of an electrospray ionization (ESI) the protein Lysozyme in vacuum was considered under the influence ofdifferent field strengths. The simulations showed three distinct patterns: (1) the protein wasdenaturated when exposed to too strong electrical fields, above 1.5 V/nm; (2) the proteinoriented without being denaturated at field strengths between 0.5 V/nm and 1.5 V/nm (3) theprotein did not orient and did not denaturate if the strength of the field became to low, below0.5 V/nm. Our simulations show that the orientation of the protein in the fields correspondingto the second pattern takes place within time intervals from about 100 ps at 1.5 V/nm to about1 ns at 0.5 V/nm. We therefore predict, that there exists a window of field strengths, which issuitable for orientation of proteins in experimental studies without affecting their structure.The orientation of proteins potentially increases the amount of information that can beobtained from experiments such as single particle imaging. This study will therefore bebeneficial for the development of such modern techniques.
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Baskaran, Preetisri. "Computer simulation of protein superabsorbents." Thesis, Högskolan i Borås, Institutionen Ingenjörshögskolan, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:hb:diva-20927.

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The aim of this project is to develop superabsorbents from proteins in our case it is azygomycetes fungus, where the process of this fungus is studied experimentally in Universityof Borås. As a result of this experiment by-products of protein are produced and this project isabout the study to make use of such proteins as superabsorbing materials.The water absorbing capacity is computationally studied using Gibbs ensemble Monte Carlo(GEMC) simulations to determine the absorbing properties and to effectively improve theabsorbing capacity by using specific treatments, where this project focuses in using mesoscaleforce fields such as the MARTINI force field instead of atomistic force fields which wereused in studying the structure of the superabsorbents.For this purpose, the program code GEMMS is modified to make it read the desirable fileformats in order to perform the simulations. C++ is used here to code the program to read theGROMACS topology file (.top) for MARTINI force field instead of, as currently reading theatom type file (.atp) and the residue type file (.rtp) for the AMBER99 atomistic force field.
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Benazieb, Othmène. "Rheology of lipids layers at molecular length scales." Thesis, Strasbourg, 2020. http://www.theses.fr/2020STRAE003.

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Les phospholipides ont sans aucun doute un rôle capital dans les propriétés de lubrification de biosystèmes. L’exemple le plus probant est le cas des contacts biologiques tels que les articulations ; celles-ci présentent un coefficient de friction très faible. La compréhension de tels systèmes biophysiques présente des enjeux aussi bien fondamentaux qu’appliqués, en lien par exemple avec l’arthrose et la confection de prothèses articulaires. Nous simulons à l’aide du moteur de dynamique moléculaire GROMACS une bicouche de lipide (DSPC) subissant une contrainte appliquée de différentes manières, et observons la réponse de la membrane en fonction de l’état (fluide ou gel) dans laquelle elle se trouve. La première méthode (« CPF : constant pull force ») consiste à appliquer un couple de forces constantes à deux sous-systèmes, et induire par conséquent une déplacement relatif stationnaire de ces deux sous-groupes. La seconde méthode («FKR : force kick relaxation ») consiste à préparer les deux sous-systèmes avec une vitesse relative finie opposée, de façon à garantir l’immobilité du centre de masse du système complet, et à suivre au cours du temps la relaxation mécanique de ces systèmes vers l’équilibre. Nous avons clairement mis en évidence un régime viscoélastique que nous attribuons à l’élasticité d’inclinaison des lipides. Dans l’état gel, nous avons découvert un régime non linéaire, correspondant à une rhéo-fluidification. Le coefficient de friction apparent b semble diminuer quand la force augmente. La bicouche dans l’état gel est donc sujette à une dynamique lente et plus complexe que dans l’état fluide. Par ailleurs notre approche a le mérite de se généraliser aux membranes supportées, pour lesquelles nous obtenons des résultats pour la diffusion et la friction des différentes couches
Phospholipids undoubtedly have a crucial role in the lubrication properties of biosystems. The most convincing example is the case of biological contacts such as human joints, which have a very low coefficient of friction. The comprehension of such biophysical systems implicates both fundamental as well as applied challenges, for instance in regard to osteoarthritis and the manufacture of joint prostheses. Using the molecular dynamics engine GROMACS, we simulate a lipid bilayer (DSPC) undergoing stress applied in different ways and observe the response of the membrane depending on the physical state (fluid or gel). The first method (CPF: constant pull force) consists in applying a pair of constant forces to two subsystems, and therefore induce a stationary relative displacement of these two subgroups. The second method (FKR: force kick relaxation) consists in preparing the two subsystems with an opposite finite relative velocity, so as to guarantee the immobility of the center of mass of the complete system, and to follow over time the mechanical relaxation of these systems towards equilibrium. The results clearly show the presence of a viscoelastic regime that we attribute to the elasticity of lipids tilt. In the gel state, we observe a nonlinear regime, corresponding to a shear thinning. The apparent friction coefficient b tends to decrease when the force increases. Therefore, the bilayer in the gel state is subject to a slow and more complex dynamics than in the fluid state. Moreover, our approach can be generalized to supported bilayers for which we obtain results on the diffusion and friction of the different layers
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Perret, Alexandre. "Etude des propriétés de transport du CO2 et de l'éthanol en solution hydroalcoolique par dynamique moléculaire classique : Application aux vins de Champagne." Thesis, Reims, 2014. http://www.theses.fr/2014REIMS024/document.

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Les travaux présentés dans ce manuscrit sont consacrés à l'étude de la diffusion du dioxyde de carbone dissous et de l'éthanol dans une solution hydroalcoolique modèle représentant le champagne. La première partie de ce travail aborde les différents formalismes de la diffusion moléculaire, ainsi que les méthodes théoriques et expérimentales utilisées pour rendre compte de ce phénomène de transport. Une attention particulière est apportée à la dynamique moléculaire en champ de forces classiques qui est utilisé dans ce travail avec le logiciel GROMACS. Cette méthode théorique procure un point de vue novateur dans la recherche sur le champagne et plus particulièrement sur le rôle de chaque espèce majoritaire dans la diffusion du CO2. La spectroscopie RMN, ainsi qu'une méthode expérimentale basée sur l'étude du taux de grossissement des bulles, ont également été utilisées. Dans la deuxième partie, les résultats théoriques et expérimentaux sont présentés et comparés entre eux afin de valider le protocole des simulations de dynamique moléculaire. Les viscosités de la solution modèle et du champagne, ainsi que les rayons hydrodynamiques du CO2 et de l'éthanol sont également étudiés. La dernière partie du manuscrit concerne le partenariat avec l'entreprise Bull et l'étude des performances du logiciel GROMACS. L'expertise des équipes de Bull, ainsi que les outils développés par l'entreprise, permettent d'étudier le passage à l'échelle (ou "scalabilité") et le comportement parallèle de GROMACS pour la modélisation du champagne
The work presented in this manuscript is devoted to the study of the diffusion of dissolved carbon dioxide and ethanol in a hydroalcoholic solution model representing Champagne wines. The first part of this work deals with the different formalisms of molecular diffusion, as well as theoretical and experimental methods used to account for this phenomenon of transport. Particular attention is paid to the classical force field molecular dynamics that is used in this work with the GROMACS software. This theoretical approach provides a new perspective in research on champagne and particularly on the role of each of the main species in CO2 diffusion. NMR spectroscopy, and an experimental method based on the study of the bubbles growth rate, were also used. In the second part, the theoretical and experimental results are presented and compared with each other to validate the protocol of molecular dynamics simulations. The viscosities of the model solution and of the champagne, as well as the hydrodynamic radii of CO2 and ethanol, are also investigated. The last part of the manuscript focuses on the partnership with the Bull company and the study of the GROMACS software performance. The expertise of and the tools developed by the Bull company are used to study the scalability and the parallel behavior of GROMACS for modeling champagne
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Cordomí, Montoya Arnau. "Molecular dynamics simulations of seven-transmembrane receptors." Doctoral thesis, Universitat Politècnica de Catalunya, 2008. http://hdl.handle.net/10803/6464.

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Seven transmembrane (7-TM) G protein coupled receptors (GPCR) constitute the largest family of integral membrane proteins in eukaryotes with more than 1000 members and encoding more than 2% of the human genome. These proteins play a key role in the transmission and transduction of cellular signals responding to hormones, neurotransmitters, light and other agonists, regulating basic biological processes. Their natural abundance together with their localization in the cell membrane makes them suitable targets for therapeutic intervention. Consequently, GPCR are proteins with enormous pharmacologic interest, representing the targets of about 50% of the currently marketed drugs.
The current limitations in the experimental techniques necessary for microscopic studies of the membrane as well as membrane proteins emerged the use of computational methods and specifically molecular dynamics simulations. The lead motif of this thesis is the study of GPCR by means of this technique, with the ultimate goal of developing a methodology that can be generalized to the study of most 7-TM as well as other membrane proteins. Since the bovine rhodopsin was the only protein of the GPCR family with a known threedimensional structure at an atomic level until very recently, most of the effort is centered in the study of this receptor as a model of GPCR.
The scope of this thesis is twofold. On the one hand it addresses the study of the simulation conditions, including the procedure as well as the sampling box to get optimal results, and on the other, the biological implications of the structural and dynamical behavior observed in the simulations. Specifically, regarding the methodological aspects of the work, the bovine rhodopsin has been studied using different treatments of long-range electrostatic interactions and sampling conditions, as well as the effect of sampling the protein embedded in different one-component lipid bilayers. The binding of ions to lipid bilayers in the absence of the protein has also been investigated.
Regarding the biological consequences of the analysis of the MD trajectories, it has been carefully addressed the binding site of retinal and its implications in the process of isomerization after photon uptake, the alteration a group of residues constituting the so-called electrostatic lock between helices TM3 and TM6 in rhodopsin putatively used as common activation mechanism of GPCR, and the structural effects caused by the dimerization based on a recent semi-empirical model. Finally, the specific binding of ions to bacteriorhodopsin has also been studied.
The main conclusion of this thesis is provide support to molecular dynamics as technique capable to provide structural and dynamical informational about membranes and membrane proteins, not currently accessible from experimental methods). Moreover, the use of an explicit lipidic environment is crucial for the study the membrane protein dynamics as well as for the protein-protein and lipidprotein interactions.
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Östlin, Christofer. "Single-molecule X-ray free-electron laser imaging : Interconnecting sample orientation with explosion data." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-231009.

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X-ray crystallography has been around for 100 years and remains the preferred technique for solving molecular structures today. However, its reliance on the production of sufficiently large crystals is limiting, considering that crystallization cannot be achieved for a vast range of biomolecules. A promising way of circumventing this problem is the method of serial femtosecond imaging of single-molecules or nanocrystals utilizing an X-ray free-electron laser. In such an approach, X-ray pulses brief enough to outrun radiation damage and intense enough to provide usable diffraction signals are employed. This way accurate snapshots can be collected one at a time, despite the sample molecule exploding immediately following the pulse due to extreme ionization. But as opposed to in conventional crystallography, the spatial orientation of the molecule at the time of X-ray exposure is generally unknown. Consequentially, assembling the snapshots to form a three-dimensional representation of the structure of interest is cumbersome, and normally tackled using algorithms to analyze the diffraction patterns. Here we explore the idea that the explosion data can provide useful insights regarding the orientation of ubiquitin, a eukaryotic regulatory protein. Through two series of molecular dynamics simulations totaling 588 unique explosions, we found that a majority of the carbon atoms prevalent in ubiquitin are directionally limited in their respective escape paths. As such we conclude it to be theoretically possible to orient a sample with known structure based on its explosion pattern. Working with an unknown sample, we suggest these discoveries could be applicable in tandem with X-ray diffraction data to optimize image assembly.
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Books on the topic "GROMACS"

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Kutuzov, K. Gromada. Moskva: OOO "Babl", 2020.

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"Gromami otrazhai͡a︡ grom-- ". Moskva: TOO IIK "Kalita", 1995.

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Koshelev, V. A. "Onegina" vozdushnai͡a︡ gromada--. Sankt-Peterburg: Akademicheskiĭ proekt, 1999.

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Dete groma. Beograd: N. Vuković, 2002.

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Mate, Maras, and Maroević Tonko 1941-, eds. Mazere =: Gromače = Muri a secco. Castel Maggiore: Book Editore, 1993.

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Os gromos do pensamento. Vigo: Galaxia, 1996.

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Kondratenko, Viktor. Malʹchiki "Groma": Povestʹ. Kiev: Rad. pysʹmennyk, 1985.

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Kondratenko, V. A. Malʹchiki "Groma": Povestʹ. Kiev: "Rad. pysʹmennyk", 1985.

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Bryksina, Tatʹi︠a︡na. V ozhidanii groma: Stikhi. Moskva: Sov. pisatelʹ, 1989.

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Šapat groma: Izbor poezije. Podgorica: Narodna biblioteka "Radoslav Ljumović", 1999.

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Book chapters on the topic "GROMACS"

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Kutzner, Carsten, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, and Helmut Grubmüller. "Improved GROMACS Scaling on Ethernet Switched Clusters." In Recent Advances in Parallel Virtual Machine and Message Passing Interface, 404–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11846802_57.

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ASC Community. "Optimization for the Molecular Dynamics Software GROMACS." In The Student Supercomputer Challenge Guide, 193–201. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-3731-3_12.

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Hernandez, Monica L., Matthieu Dreher, Carlos J. Barrios, and Bruno Raffin. "Asynchronous in Situ Processing with Gromacs: Taking Advantage of GPUs." In Communications in Computer and Information Science, 89–106. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-26928-3_7.

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Tang, Xudong, Tao Wu, Tiejun Wang, and Jiliang Wu. "Molecular Dynamics Simulation Optimization Based on GROMACS on Sunway TaihuLight." In Lecture Notes in Computer Science, 112–23. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-24265-7_10.

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Zalevsky, Arthur O., Roman V. Reshetnikov, and Andrey V. Golovin. "New QM/MM Implementation of the MOPAC2012 in the GROMACS." In Communications in Computer and Information Science, 279–88. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-05807-4_24.

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Páll, Szilárd, Mark James Abraham, Carsten Kutzner, Berk Hess, and Erik Lindahl. "Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS." In Lecture Notes in Computer Science, 3–27. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-15976-8_1.

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Markov, S., P. Petkov, and V. Pavlov. "Large-Scale Molecular Dynamics Simulations on Modular Supercomputer Architecture with Gromacs." In Advances in High Performance Computing, 359–67. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-55347-0_30.

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Chen, Yu Wai, Yong Wang, Yun-Chung Leung, and Kwok-Yin Wong. "Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen." In Methods in Molecular Biology, 277–88. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0892-0_16.

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Costantini, Alessandro, Eduardo Gutierrez, Javier Lopez Cacheiro, Aurelio Rodriguez, Osvaldo Gervasi, and Antonio Laganà. "Porting of GROMACS Package into the Grid Environment: Testing of a New Distribution Strategy." In Computational Science and Its Applications – ICCSA 2010, 41–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12189-0_4.

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Yu, Yang, Hong An, Junshi Chen, Weihao Liang, Qingqing Xu, and Yong Chen. "Pipelining Computation and Optimization Strategies for Scaling GROMACS on the Sunway Many-Core Processor." In Algorithms and Architectures for Parallel Processing, 18–32. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65482-9_2.

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Conference papers on the topic "GROMACS"

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Goga, Nicolae, Iuliana Marin, Andrei Vasilateanu, Ionel-Bujorel Pavaloiu, Kamoru Oluwatoyin Kadiri, and Oludele Awodele. "Improved GROMACS algorithms using the MPI parallelization." In 2015 E-Health and Bioengineering Conference (EHB). IEEE, 2015. http://dx.doi.org/10.1109/ehb.2015.7391443.

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Alekseenko, Andrey, Szilárd Páll, and Erik Lindahl. "Experiences With Adding SYCL Support to GROMACS." In IWOCL'21: International Workshop on OpenCL. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3456669.3456690.

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Goga, Nicolae, Siewert Marrink, Stefania Victoria Costache, and Florica Moldoveanu. "Multiscaling algorithms for molecular dynamics simulations with GROMACS." In 2009 3rd Annual IEEE Systems Conference. IEEE, 2009. http://dx.doi.org/10.1109/systems.2009.4815825.

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Páll, Szilárd, and Roland Schultz. "Advances in the OpenCL offload support in GROMACS." In IWOCL'19: International Workshop on OpenCL. New York, NY, USA: ACM, 2019. http://dx.doi.org/10.1145/3318170.3318176.

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Sarkar, Arkadeep, Lucia Sessa, Luigi Di Biasi, and Stefano Piotto. "YAMACS: A Python Based Tool Kit for GROMACS." In ECMC 2022. Basel Switzerland: MDPI, 2022. http://dx.doi.org/10.3390/ecmc2022-13433.

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Wagner, Michael, Jens Doleschal, and Andreas Knupfer. "Tracing long running applications: A case study using Gromacs." In 2015 International Conference on High Performance Computing & Simulation (HPCS). IEEE, 2015. http://dx.doi.org/10.1109/hpcsim.2015.7237031.

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Garces, Nathalia, Harold Castro, Paula Delgado, Andres Gonz'lez, Carlos A. Jaramillo, Natalia Penaranda, and Maria del Pilar Delgado. "Analysis of Gromacs MPI Using the Opportunistic Cloud Infrastructure UnaCloud." In 2012 Sixth International Conference on Complex, Intelligent, and Software Intensive Systems (CISIS). IEEE, 2012. http://dx.doi.org/10.1109/cisis.2012.142.

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Olivier, Stephen, Jan Prins, Jeff Derby, and Ken Vu. "Porting the GROMACS Molecular Dynamics Code to the Cell Processor." In 2007 IEEE International Parallel and Distributed Processing Symposium. IEEE, 2007. http://dx.doi.org/10.1109/ipdps.2007.370560.

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Li, Ce, Wenbo Chen, Yang Zhang, and Qifeng Bai. "Analyses on Performance of Gromacs in Hybrid MPI+OpenMP+CUDA Cluster." In 2014 IEEE International Conference on High Performance Computing and Communications (HPCC), 2014 IEEE 6th International Symposium on Cyberspace Safety and Security (CSS) and 2014 IEEE 11th International Conference on Embedded Software and Systems (ICESS). IEEE, 2014. http://dx.doi.org/10.1109/hpcc.2014.157.

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Goga, Nicolae, Siewert Marrink, Ruxandra Cioromela, and Florica Moldoveanu. "GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations." In 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE). IEEE, 2012. http://dx.doi.org/10.1109/bibe.2012.6399683.

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Reports on the topic "GROMACS"

1

Junghans, Christoph, Joshua Phillips, and Michael Wall. Gromacs IC Tutorial. Office of Scientific and Technical Information (OSTI), July 2014. http://dx.doi.org/10.2172/1136453.

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