1 / 5

Molecular dynamics Calculations in NAMD

Molecular dynamics Calculations in NAMD. Dr Karina Kubiak - Ossowska High Performance Computing Support Team Department of Physics e-mail: karina.kubiak@strath.ac.uk. NAMD. NAMD web page: http://www.ks.uiuc.edu/Research/namd/ Documentation: http://www.ks.uiuc.edu/Research/namd/2.7/ug/

shawnak
Download Presentation

Molecular dynamics Calculations in NAMD

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Molecular dynamics Calculations in NAMD Dr Karina Kubiak - Ossowska High Performance Computing Support Team Department of Physics e-mail: karina.kubiak@strath.ac.uk

  2. NAMD NAMD web page: http://www.ks.uiuc.edu/Research/namd/ Documentation: http://www.ks.uiuc.edu/Research/namd/2.7/ug/ http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf NAMD is ia parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code.

  3. Before you start… Example files location on ARCHIE-WeSt: /users/cwb08102/NAMD_Training Load the modules: module load /apps/bin/vmd/1.9.1 module load /mpi/gcc/openmpi/1.4.5 module load /libs/gcc/fftw2/float-mpi/2.1.5 module load /apps/gcc/namd/mpi/2.8

  4. Simulations in NAMD Now we will follow the manual and will run sample simulations remotely on ARCHIE-WeSt.

More Related