排序方式: 共有24条查询结果,搜索用时 15 毫秒
1.
2.
Miller BT Singh RP Klauda JB Hodoscek M Brooks BR Woodcock HL 《Journal of chemical information and modeling》2008,48(9):1920-1929
A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used to implement the web application is described. Two additional programs have been developed and integrated with CHARMMing: GENRTF, which is employed to define structural features not supported by the standard CHARMM force field, and a job broker, which is used to provide a portable method for using grid and cluster computing with CHARMMing. The use of the program is described with three proteins: 1YJP , 1O1O , and 1UFY . Source code is provided allowing CHARMMing to be downloaded, installed, and used by supercomputing centers and research groups that have a CHARMM license. Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations. 相似文献
3.
4.
5.
Simple Zeros of the Riemann Zeta-Function 总被引:1,自引:0,他引:1
Assuming the Riemann Hypothesis, Montgomery showed by meansof his pair correlation method that at least two-thirds of thezeros of Riemann's zeta-function are simple. Later he and Taylorimproved this to 67.25 percent and, more recently, Cheer andGoldston increased the percentage to 67.2753. Here we proveby a new method that if the Riemann and Generalized LindelöofHypotheses hold, then at least 70.3704 percent of the zerosare simple and at least 84.5679 percent are distinct. Our methoduses mean value estimates for various functions defined by Dirichletseries sampled at the zeros of the Riemann zeta-function. 1991Mathematics Subject Classification: 11M26. 相似文献
6.
This paper concerns a Markov operator T on a space L1, and aMarkov process P which defines a Markov operator on a spaceM of finite signed measures. For T, the paper presents necessaryand sufficient conditions for:
- a the existence of invariant probabilitydensities (IPDs)
- b the existence of strictly positive IPDs,and
- c the existence and uniqueness of IPDs.
- b the existence of strictly positive IPDs,and
7.
8.
High-level ab initio quantum mechanical calculations are used to study various gauche conformational energies of n-pentane to n-decane. The destabilizing "pentane effect" (adjacent gauche states of opposite sign) for alkanes is confirmed, but the energies were found to depend slightly on chain length. In contrast, introducing an adjacent gauche of the same sign requires only 0.22-0.37 kcal/mol, approximately half of the single gauche state energy. This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers. 相似文献
9.
Emilia L. Wu Xi Cheng Sunhwan Jo Huan Rui Kevin C. Song Eder M. Dávila‐Contreras Yifei Qi Jumin Lee Viviana Monje‐Galvan Richard M. Venable Jeffery B. Klauda Wonpil Im 《Journal of computational chemistry》2014,35(27):1997-2004
CHARMM‐GUI Membrane Builder, http://www.charmm‐gui.org/input/membrane , is a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance‐based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM‐GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc. 相似文献
10.