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|5352 次阅读|没有评论

constrain optimization in Gaussion

袁曙光 2012-3-13 02:05

It would be necessary to restrain bond length or dihedral angle when optimizing geometry of ligand to avoid intra-molecular hydrogen bonds and transition state type structures. here is some description of restrain in Gaussian. from http://www.gaussian.com/g_tech/g_ur/k_opt.htm Opt DESCRIPT ...

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Progress of present GPCR structure

袁曙光 2012-3-12 15:15

from stevens.scripps.edu

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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 ----- ...

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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|6014 次阅读|5 个评论 热度 2

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 ...

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GPCR phylogenetics tree

热度 1 袁曙光 2011-7-29 17:52

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Science Arts 2

袁曙光 2011-7-19 04:02

DNA Binds to Protein ABT-737 Binds to Bcl-XL Antagonist Binds to GPCR

个人分类: 科研笔记|3739 次阅读|没有评论

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