نتایج جستجو برای: namd
تعداد نتایج: 319 فیلتر نتایج به سال:
Based on the previous studies of RNA nanorings, in this contribution we computationally analyze the structure and properties of RNA nanotubes, where we focus on nanotubes consisting of up to five nanorings of around 20nm in diameter. We have developed a molecular dynamics (MD) method and implemented it by using the NAMD and VMD packages in a high-performance computing environment to study the s...
UNLABELLED birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in pa...
References Conclusion Methodology The structures given by CAPRI organizers for target 34 were the bound structure of the RNA molecule and the structure of an homologous protein. First, it was necessary to model the protein that interacts with the RNA by homology. To do that, we used the MODELLER program coupled with a minimization of 6400 steps using CHARMM force field. Then, we used the HEX pr...
SUMMARY MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of ...
Pathological neovascularization of the outer retina is the hallmark of neovascular age-related macular degeneration (nAMD). Building on our previous observations that semaphorin 3F (Sema3f) is expressed in the outer retina and demonstrates anti-angiogenic potential, we have investigated whether Sema3f can be used to protect against subretinal neovascularization in two mouse models. Both in the ...
The use of Simultaneous Multithreading (SMT) on HPCx is investigated to determine if any performance improvement is obtainable for user applications. Various codes are benchmarked with and without the use of SMT. SMT is seen to boost the performance, at low and moderate processor counts, of the H2MOL application and the classical molecular dynamics codes NAMD, MDcask and DL POLY, with up to a f...
FPGA-centric clusters use FPGAs for both computation and communication and thereby address three fundamental problems of future High Performance Clusters: efficient use of silicon, power, and removing communication bottlenecks. In this study we report on the plausibility of using such clusters for Molecular Dynamics simulations, in particular by determining the communication requirements for su...
LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, ...
MPI and Charm++ embody two distinct perspectives for writing parallel programs. While MPI provides a processor-centric, user-driven model for developing parallel codes, Charm++ supports work-centric, overdecompositionbased, system-driven parallel programming. One or the other can be the best or most natural fit for distinct modules that constitute a parallel application. In this paper, we prese...
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