namd

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 namd [2014/06/17 11:14]noskov namd [2020/10/02 15:05]jrutte02 removed 2020/10/02 15:05 jrutte02 removed2018/08/18 06:12 meesters 2018/05/04 17:14 noskov 2018/05/04 17:13 noskov 2017/09/18 11:38 meesters 2014/06/17 15:00 noskov 2014/06/17 14:59 noskov 2014/06/17 14:59 noskov 2014/06/17 12:49 noskov 2014/06/17 12:39 noskov 2014/06/17 12:32 noskov 2014/06/17 12:31 noskov 2014/06/17 12:21 noskov 2014/06/17 12:20 noskov 2014/06/17 11:57 noskov 2014/06/17 11:53 noskov 2014/06/17 11:42 noskov 2014/06/17 11:41 noskov 2014/06/17 11:36 noskov 2014/06/17 11:24 noskov 2014/06/17 11:14 noskov 2014/06/17 11:14 noskov 2014/06/17 11:06 noskov 2014/06/17 11:05 noskov 2014/06/17 10:54 noskov 2014/06/17 10:53 noskov 2014/06/17 10:50 noskov created 2020/10/02 15:05 jrutte02 removed2018/08/18 06:12 meesters 2018/05/04 17:14 noskov 2018/05/04 17:13 noskov 2017/09/18 11:38 meesters 2014/06/17 15:00 noskov 2014/06/17 14:59 noskov 2014/06/17 14:59 noskov 2014/06/17 12:49 noskov 2014/06/17 12:39 noskov 2014/06/17 12:32 noskov 2014/06/17 12:31 noskov 2014/06/17 12:21 noskov 2014/06/17 12:20 noskov 2014/06/17 11:57 noskov 2014/06/17 11:53 noskov 2014/06/17 11:42 noskov 2014/06/17 11:41 noskov 2014/06/17 11:36 noskov 2014/06/17 11:24 noskov 2014/06/17 11:14 noskov 2014/06/17 11:14 noskov 2014/06/17 11:06 noskov 2014/06/17 11:05 noskov 2014/06/17 10:54 noskov 2014/06/17 10:53 noskov 2014/06/17 10:50 noskov created Line 1: Line 1: - ====== High-performance simulation of large bimolecular systems - NAMD ====== + ====== Using VMD and NAMD on Mogon ====== + ===== Licensing Issues ===== - NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. + We, the ZDV HPC group, will setup and compile [[http://www.ks.uiuc.edu/Research/vmd/|VMD]] and [[http://www.ks.uiuc.edu/Research/namd/|NAMD]] for you -- [[https://hpc.uni-mainz.de/high-performance-computing/service-angebot/softwareinstallation/|upon request]]. You will find the installed modules as - Documentation and source code on the web page of "[[http://www.ks.uiuc.edu/Research/namd/|Theoretical and computational biophysics group]]" + - There are few possibilities to start NAMD simulation on the MOGON cluster. + - If + vis/VMD/ + chem/NAMD/ + + + Here, the '''' may deviate between the clusters. If you are missing a particular version, please inform us. + + + Both, VMD and NAMD, come with a license, which prohibits us to //just install//. We, therefore, need individual users to print and sign the linked licenses ([[http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html|VMD license]] and [[http://www.ks.uiuc.edu/Research/namd/license.html|NAMD license]]) on that paper. Subsequently, send it via internal mail ("Hauspost") to "ZDV HPC group". We will then set the permissions accordingly. + + When doing so, please include: + * your name + * your username + * your email address (in case we need to approach you) + + + ===== Using VMD ===== + + + We generally do not provide support in using a particular software with all its flags (or in the case of a GUI, all its clicks). In this particular case we refer to the [[http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html|VMD tutorial]]. + + + That being written, we are aware that starting the VMD-GUI can be tricky and the relevant information hard to find. + + ==== Starting the graphical user interface (GUI) ==== + + Here, we give some brief snippets, covering the essentials: + + * First, we need to load the module and instruct VMD to start in its graphical, non-MPI mode: + + + $module load vis/VMD # this will load the most current version, which is installed +$ export VMDNOMPI=1 + + + * Next, we start an interactive session, e.g. with ''salloc''. Here is a little more information on [[slurm_submit#interactive_jobs|interactive jobs]]. With respect to the number of cpus: Not everything in VMD is parallelized. If you want to start an VMD-MPI job, you better write a VMD script and start VMD [[slurm_submit#simple_mpi_job|like a conventional MPI-application]]. + + + $salloc -A -p short -c -t + +$ srun vmd + + + * When ending the session, do not forget to type ''exit'' to relinquish the allocation. + + ==== Setting up a simulation files for NAMD ==== + + + Molecular Dynamics (MD) simulations can be tricky to be set up correctly. It is not unusual to make mistakes, which may consume lots of CPU time. The purpose of these snippets is not to teach running MD simulations in all detail, but to descript how to generate the most basic setup. + + + The following section refers to [[http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node6.html|the VMD tutorial section on generating a PSF file]]: + + - load a new molecule + - run the autopsf utility (Extensions -> Modeling -> Automatic PSF Builder) + + This will create the following files: ''_autopsf_formatted.pdb'', ''molecule_prefix>_autopsf.log'', ''_autopsf.pdb'', ''_autopsf.psf''. + + Of course, VMD offers many more options, most are more sophisticated than this description. + + ===== Using NAMD ===== + + With a given [[http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html|configuration file]], you **can** start NAMD like this: + + + #!/bin/bash + + #SBATCH -t + + The configuration file content depends on the simulation to be carried out, however, the ''coordinates'' and ''structure'' parameters could simply refer to the autogenerated ''.pdf'' and ''.psf'' files produced by VMD as described, respectively.