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分享 The Nobel Prize in Chemistry 2012 was awarded to GPCR study
袁曙光 2012-10-10 18:40
The Nobel Prize in Chemistry 2012 was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka "for studies of G-protein-coupled receptors (GPCR) http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2012/ Robert J. Lefkowitz Born: 194 ...
个人分类: 科研笔记|2867 次阅读|没有评论
分享 Back from CECAM workshop
热度 2 袁曙光 2012-10-5 15:07
Back from CECAM workshop
The recent CECAM workshop "High Performance Computing in Computational Chemistry and Molecular Biology: Challenges and Solutions Provided by ScalalLife Project" seems to be like Gromacs developer and users reunion meeting since it mainly focus on Gromacs and related topic. Lots of Gromacs guy ...
个人分类: 科研笔记|2353 次阅读|2 个评论 热度 2
分享 Dedicated stategies for GPCR MD simulation
袁曙光 2012-7-27 02:43
As the most important membrane protein, GPCR MD simulation is a quite hot topic nowadays. However, how to assemble protein/membrane system and which forcefield to assign for the whole system are two main critical and tough task for GPCR simulations. 1. Assemble protein/membrane system ...
个人分类: 科研笔记|5990 次阅读|没有评论
分享 compile Desmond from source code
袁曙光 2012-4-15 22:02
As a highly optimized parallel MD tool, compiled Desmond is around 20-30% faster than the pre-compiled version which is distrubuted in Schrodinger software. here are some steps for how to compile Desmond from source code. 1. download source code from http://www.deshawresearch.com/resources_desmond. ...
个人分类: 科研笔记|4214 次阅读|没有评论
分享 Progress of present GPCR structure
袁曙光 2012-3-12 15:15
Progress of present GPCR structure
from stevens.scripps.edu
个人分类: 科研笔记|2571 次阅读|没有评论
分享 The art of mMAYA
袁曙光 2011-11-18 15:41
The art of mMAYA
个人分类: 科研笔记|3786 次阅读|没有评论
分享 Tips for Desmond
袁曙光 2011-9-19 10:16
---------------Restrain atoms --------------- restrain = { atom = "asl:(chain.name A) AND (atom.ptype CA)" force_constant = 10.0 } constraining protein CA or backbone is of great use when MD is producing based on homology models. ---------------Extract trajectory ----- ...
个人分类: 科研笔记|4121 次阅读|没有评论
分享 SLI 技术在GPU计算的应用
热度 2 袁曙光 2011-9-8 01:54
最近给实验室的工作站装系统,用了SLES 11 SP1版本。机器本身采用了2块超级强悍的GPU: NVIDIA GTX 590 系统安装之后显卡驱动通常SUSE可以自动根据NVIDIA的安装源安装。奇怪的是,安装完之后一直进不了系统,根据提示应当是驱动配置的问题。 通过YAST查看驱动,SUSE不但安装好了驱动,还将NVIDIA的GPU计算程序也一并装好 ...
个人分类: 科研笔记|4615 次阅读|5 个评论 热度 2
分享 Rosetta parallel installation and job running
袁曙光 2011-8-9 21:05
Installation: A) Install MPI. B) Make sure that the mpi compilers (mpicc?) are in the path visible to SCons; if they don't install to the standard place that the normal user can see, then you can try going into rosetta_source/tools/build and copying th ...
个人分类: 科研笔记|3999 次阅读|没有评论
分享 Science Arts 2
袁曙光 2011-7-19 04:02
Science Arts 2
DNA Binds to Protein ABT-737 Binds to Bcl-XL Antagonist Binds to GPCR
个人分类: 科研笔记|2937 次阅读|没有评论

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