One step forward

HOLEhttp://s3.smartsci.uk/hole2/doc/index.html Transmembrane protein pore radius analysis tool

Wikipediahttps://en.wikipedia.org/wiki/Fatty_acid VMD analysishttp://www.ks.uiuc.edu/Training/CaseStudies/pdfs/bilayer.pdf Paper(carbon numbering)Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions

Tutorial pointhttp://www.tutorialspoint.com/python Python Practice bookhttp://anandology.com/python-practice-book/iterators.html 한글 Wikidocshttps://wikidocs.net/14 Biopython 관련 자료http://fenyolab.org/ibb2015/pdf/IBB2015_homework4_biopython.pdf

Analyze Big DCD Fielshttp://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/ MDAnalysis(Python package)http://pythonhosted.org/MDAnalysis/index.html1. Overview over MDAnalysis2. Selection Commands3. Analysis modules4. Topology modules5. Coordinates modules6. Selection exporters7. Core modules8. Visualization modules9. MDAnalysis library10. Version information for MDAnalysis — MDAnalys..

NAMDMembrane related researcheshttp://bionano.physics.illinois.edu/Tutorials/ Case studieshttp://www.ks.uiuc.edu/Training/CaseStudies/

Mounting sharing folder from Windows to Linux1. Make sure that the target folder is shared on VirtualBox setting.Refer below (http://www.liberiangeek.net/2012/05/access-virtualbox-shared-folder-from-ubuntu-12-04-precise-pangolin-guest-machine/)If you’ve been following this blog, then you probably know a thing or two about VirtualBox. That’s because we’ve written a lot about it. If you don’t know..

자세한건 http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node7.html Data Analysis of DCD result fileOpen the script file distance.tcl with a text editor. You can see that the script does the following:Choose atom selections set sel1 [atomselect top "$seltext1"] set sel2 [atomselect top "$seltext2"] Get the number of frames in the trajectory and assign this value to the variable nf set nf..

시뮬레이션을 돌리다보면 SSH 연결이 끊어지는 경우가 발생한다. 이럴때 문제가 돌고 있던 시뮬레이션도 종료 되버린다는 것. 그래서 SSH 세션 종료후에도 작업하던것 살려놓는 방법이 있어야 하는데 Google에서 찾아보니 screen이라는 것을 통해서 살려 놓는 방법이 있음.. 아래는 그 내용 http://www.howtogeek.com/howto/ubuntu/keep-your-ssh-session-running-when-you-disconnect/ Keep Your SSH Session Running when You DisconnectScreen is like a window manager for your console. It will allow you to keep multiple terminal se..

GPU 가속namd2 +idlepoll +p64 step6.6_equilibration.inphttp://www.ks.uiuc.edu/Research/namd/2.9/ug/node88.html lmp_serial -sf gpu -pk gpu 64 -in in.flowhttp://lammps.sandia.gov/doc/accelerate_gpu.html 멀티노드 가속namd2 +p charmrun namd2 ++local +p ~/NAMD_2.10_Linux-x86_64/charmrun ~/NAMD_2.10_Linux-x86_64/namd2 +p64 ++nodelist ~/NAMD_2.10_Linux-x86_64/hostfile.txt ./step7.1_production.inp

포토스케이프: 연속된 이미지를 GIF로 oCAM: 화면을 녹화해서 동영상 파일로 (AVI, MP4, WMV 등등) ScreentToGif: 화면을 녹화해서 GIF로 다음팟 인코더: 동영상 편집해서 저장 또는 파일 포맷 변경