MOIL: A program for simulations of macromolecules

Elber, Ron; Roitberg, Adrián E.; Simmerling, Carlos; Goldstein, Robert F.; Li, Haiying; Verkhivker, Gennady M.; Keasar, Chen; Zhang, Jing; Ulitsky, Alex

doi:10.1016/0010-4655(95)00047-j

Cited by 157 publications

(189 citation statements)

References 18 publications

Supporting

Mentioning

186

Contrasting

Order By: Relevance

“…The estimates are based on the MOIL program (Elber, Roitberg et al 1995) (see section on Numerical Examples below), though similar numbers are expected for other programs as well. If the fast degrees of freedom (e.g.…”

Section: Introductionmentioning

confidence: 57%

“…The conjugate gradient algorithm converges rapidly and is relatively easy to parallelize. The algorithm is implemented in MOIL (Elber, Roitberg et al 1995), a publicly available molecular dynamics suite of programs (http://cbsu.tc.cornell.edu/software/moil). Our algorithm is exact in the sense that a parallel and a serial version are guaranteed to give the same answer.…”

Section: Discussion and Summarymentioning

confidence: 99%

“…The parallel SHAKE algorithm discussed above was implemented in the program MOIL (Elber, Roitberg et al 1995 When the SHAKE algorithm was used we also parallelize the Verlet integrator. For the systems we investigate, the number of SHAKE iterations that were required never exceeded 4.…”

Section: Numerical Experimentsmentioning

confidence: 99%

See 2 more Smart Citations

Revisiting and parallelizing SHAKE

Weinbach

Elber

2005

Journal of Computational Physics

Self Cite

102

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 57%

Section: Discussion and Summarymentioning

confidence: 99%

See 1 more Smart Citation

Revisiting and parallelizing SHAKE

Weinbach

Elber

2005

Journal of Computational Physics

Self Cite

102

View full text Add to dashboard Cite

“…Calculations of the normal modes were carried out with MOIL (53). In terms of the normal modes, the IR absorbance for a transition in mode ␣, with n␣ vibrational quanta to n ␣ ϩ 1 vibrational quanta can be estimated in terms of the mode-specific dipole derivative (45,58).…”

Section: Methodsmentioning

confidence: 99%

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

Heugen

Schwaab

Bründermann

et al. 2006

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

383

331

View full text Add to dashboard Cite

Hydrogen bond rearrangement in water occurs on the picosecond time scale, so relevant experiments must access these times. Here, we show that terahertz spectroscopy can directly investigate hydration layers. By a precise measurement of absorption coefficients between 2.3 THz and 2.9 THz we could determine the size and the characteristics of the hydration shell. The hydration layer around a carbohydrate (lactose) is determined to extend to 5.13 ؎ 0.24 Å from the surface corresponding to Ϸ123 water molecules beyond the first solvation shell. Accompanying molecular modeling calculations support this result and provide a microscopic visualization. Terahertz spectroscopy is shown to probe the collective modes in the water network. The observed increase of the terahertz absorption of the water in the hydration layer is explained in terms of coherent oscillations of the hydration water and solute. Simulations also reveal a slowing down of the hydrogen bond rearrangement dynamics for water molecules near lactose, which occur on the picosecond time scale. The present study demonstrates that terahertz spectroscopy is a sensitive tool to detect solute-induced changes in the water network.hydration water dynamics ͉ molecular dynamics simulations of biomolecules ͉ solvated lactose T he many unusual properties of water combined with its importance as the solvent of life account for its continued study by numerous researchers. Indeed, the properties of water are essential in the behavior of all biological systems. For example, water plays a central role in the folding and function of proteins, and the function of carbohydrates. The dynamics of water surrounding a solute is of fundamental importance in a wide range of processes in solution. In particular, the properties of water molecules near the surface of a biomolecule have been the subject of numerous and sometimes controversial experimental and theoretical studies (1-5). The characteristics and role of this ''biological'' water, with properties that differ considerably from those of bulk water, are still not fully understood (6).The importance of the hydration layer or the biological water is obvious in specific protein processes, such as opening and closing of channels, the kinetics of which has been found to be coupled with the solvent fluctuations (1). Important questions that remain so far unanswered include the following: How does solvation water differ from bulk water, and how large is the solvation layer that can be attributed to solvent water? Simulations suggest the existence of rather rigid water structures around proteins (5) and carbohydrates (7), but experimental studies that characterize the hydration layer are limited. Hydrogen bond rearrangements in water occur on the picosecond time scale (8), so that a detailed understanding of the relevant processes at a molecular level requires experimental techniques that are able to probe the hydration layers on this time scale. However, experimental investigations of fast dynamics of hydration water still remain a ch...

show abstract

“…Molecular dynamics (MD) simulations were performed on one molecule of H64V and 3483 rigid TIP3P water molecules 46 using the MOIL software package. 47 The MOIL force field 47 describes covalent interactions with the AMBER potential, 48 nonbonded interactions with the OPLS potential, 49 and improper torsions with the CHARMM potential. 50 Protein and solvent were contained within a 45 Å × 54 Å × 61 Å cell, subject to periodic boundary conditions.…”

Section: Experimental and Computational Methodsmentioning

confidence: 99%

Ultrafast Dynamics of Myoglobin without the Distal Histidine: Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

et al. 2005

View full text Add to dashboard Cite

Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by ∼50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.

show abstract

MOIL: A program for simulations of macromolecules

Cited by 157 publications

References 18 publications

Revisiting and parallelizing SHAKE

Revisiting and parallelizing SHAKE

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

Ultrafast Dynamics of Myoglobin without the Distal Histidine: Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

Contact Info

Product

Resources

About