Wordom: a program for efficient analysis of molecular dynamics simulations

“…An equilibrium ensemble with the cross-linker in the cis conformation was sampled by two runs of replica exchange MD (44). After instantaneously switching the torsional potential of the central N ϭ N bond to one that strongly favors the trans-configuration, ensembles of nonequilibrium Langevin dynamics runs of 4 s each were started from the cis equilibrium ensemble at both 330 K and 281 K. Network analysis (22,29) of the resulting nonequilibrium trajectories was supported by the program WORDOM (45). Because of the implicit solvent model, both the absolute temperatures and rates are somewhat arbitrary.…”

Section: Methodsmentioning

confidence: 99%

α-Helix folding in the presence of structural constraints

Ihalainen¹,

Paoli

Muff

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

116

169

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We have investigated the site-specific folding kinetics of a photoswitchable cross-linked ␣-helical peptide by using single 13 C ‫؍‬ 18 O isotope labeling together with time-resolved IR spectroscopy. We observe that the folding times differ from site to site by a factor of eight at low temperatures (6°C), whereas at high temperatures (45°C), the spread is considerably smaller. The trivial sum of the site signals coincides with the overall folding signal of the unlabeled peptide, and different sites fold in a noncooperative manner. Moreover, one of the sites exhibits a decrease of hydrogen bonding upon folding, implying that the unfolded state at low temperature is not unstructured. Molecular dynamics simulations at low temperature reveal a stretched-exponential behavior which originates from parallel folding routes that start from a kinetically partitioned unfolded ensemble. Different metastable structures (i.e., traps) in the unfolded ensemble have a different ratio of loop and helical content. Control simulations of the peptide at high temperature, as well as without the cross-linker at low temperature, show faster and simpler (i.e., single-exponential) folding kinetics. The experimental and simulation results together provide strong evidence that the rate-limiting step in formation of a structurally constrained ␣-helix is the escape from heterogeneous traps rather than the nucleation rate. This conclusion has important implications for an ␣-helical segment within a protein, rather than an isolated ␣-helix, because the cross-linker is a structural constraint similar to those present during the folding of a globular protein.cooperativity ͉ infrared spectroscopy ͉ molecular dynamics simulation ͉ peptide folding

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“…This can be done during post processing on the trajectory file, much like a conventional analysis tool, or on-the-fly during the simulation. Other software is available for analyzing existing trajectories [7,20,21,22,23,24] or for biasing MD simulations [15,9,25,26,27,7,6]. PLUMED 2, however, is the only code we know of that allows users to do both sets of tasks with a single syntax.…”

Section: Plumed 2 Overviewmentioning

confidence: 99%

PLUMED 2: New feathers for an old bird

Tribello

Bonomi

Branduardi

et al. 2014

Computer Physics Communications

2,790

2,841

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Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardwares, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here -a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

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Wordom: a program for efficient analysis of molecular dynamics simulations

Cited by 262 publications

References 13 publications

Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

α-Helix folding in the presence of structural constraints

PLUMED 2: New feathers for an old bird

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