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namd [2014/06/17 12:20]
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 ======
  
 +===== Licensing Issues =====
  
-NAMDrecipient 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. +Wethe ZDV HPC groupwill 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.+<code bash> 
 +vis/​VMD/<​version_string>​ 
 +chem/NAMD/<​version_string>​ 
 +</​code>​
  
-//<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>//+Here, the ''​<version_string>''​ may deviate between the clusters. If you are missing a particular version, please inform us.
  
-This starts one threaded simulation direkt on the login host. Input configuration file describes simulationComplete description of the input file format is available in the [[http://​www.ks.uiuc.edu/​Research/​namd/2.9/ug/node9.html|NAMD ​Documentation]].+<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.
  
-Using threaded start allows ​to achieve performance increasing: +When doing so, please include: 
-//bsub -R "​affinity[core(<number of cores>)]" ​<PATH TO NAMD INSTALLATION>/namd2 +p<number of threads> <input configuration file>// +  * your name 
-where <number of threadsis number of threads ​normally this parameter ​is equal to <number of cores>. +  * your username 
-For example +  * your email address (in case we need to approach you) 
-//bsub -R "​affinity[core(16)]" ​<PATH TO NAMD INSTALLATION>/namd2 +p 16 <input configuration file>//​ +</​WRAP>​ 
-starts NAMD simulation ​with 16 threads using 16 cores of a node.+ 
 +===== 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 mistakeswhich 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.
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