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namd [2018/05/04 17:14]
noskov
namd [2018/08/18 06:12] (current)
meesters
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-===== High-performance simulation of large bimolecular systems - NAMD =====+====== Using VMD and NAMD on Mogon ======
  
-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. +===== Licensing Issues =====
-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.+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
  
-//<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>//+<code bash> 
 +vis/VMD/<version_string> 
 +chem/NAMD/<version_string> 
 +</code>
  
-This starts one threaded simulation direkt on the login host. Input configuration file describes simulation. Complete description of the input file format is available in the [[http://​www.ks.uiuc.edu/​Research/​namd/​2.9/​ug/​node9.html|NAMD Documentation]].+Here, the ''<​version_string>''​ may deviate between ​the clustersIf you are missing a particular version, please inform us.
  
-=== Memory Usage ===+<WRAP center round info 90%> 
 +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.
  
-NAMD has traditionally used less than 100MB of memory even for systems +When doing so, please include: 
-of 100,000 atoms. ​ With the reintroduction of pairlists ​in NAMD 2.5, however, memory usage for a 100,000 atom system with a 12A cutoff can approach ​300MB, and will grow with the cube of the cutoff. ​ This extra memory is distributed across processors during a parallel run, but a single workstation may run out of physical memory with a large system.+  ​* your name 
 +  * your username 
 +  * your email address (in case we need to approach ​you) 
 +</​WRAP>​
  
 +===== Using VMD =====
 +
 +<WRAP center round important 90%>
 +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]].  ​
 +</​WRAP>​
 +
 +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:
 +
 +<code bash>
 +$ module load vis/VMD # this will load the most current version, which is installed
 +$ export VMDNOMPI=1
 +</​code>​
 +
 +  * 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]]. ​
 +
 +<code bash>
 +$ salloc -A <​your_account>​ -p short -c <​number_of_cpus>​ -t <​sufficient_time>​
 +<​snipping wainting for the session>
 +$ srun vmd <​arguments>​
 +</​code>​
 +
 +  * When ending the session, do not forget to type ''​exit''​ to relinquish the allocation.
 +
 +==== Setting up a simulation files for NAMD ====
 +
 +<WRAP center round important 90%>
 +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.
 +</​WRAP>​
 +
 +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: ''<​molecule_prefix>​_autopsf_formatted.pdb'',​ ''​molecule_prefix>​_autopsf.log'',​ ''<​molecule_prefix>​_autopsf.pdb'',​ ''<​molecule_prefix>​_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:
 +
 +<code bash>
 +#!/bin/bash
 +
 +#SBATCH -t <​time>​
 +#SBATCH -p <​partition>​ # e.g. nodeshort / parallel
 +#SBATCH -A <​account>​
 +#SBATCH -N <rather start with a low number to test>
 +#SBATCH -n <N * cores / node>
 +
 +module purge
 +
 +module load chem/NAMD
 +
 +# the suffix '​namd_conf'​ is arbitrary
 +srun namd2  <​prefix>​.namd_conf
 +</​code>​
 +
 +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.
namd.txt · Last modified: 2018/08/18 06:12 by meesters