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namd [2018/05/04 17:13]
noskov
namd [2018/08/18 06:12]
meesters
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-===== High-performance simulation of large bimolecular systems - NAMD =====+====== Using VMD and NAMD on Mogon ======
  
-<WRAP center round todo 90%> +===== Licensing Issues ===== 
-''​This page is outdated. We hope to provide more informationsoon.''​+ 
 +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 
 + 
 +<code bash> 
 +vis/​VMD/<​version_string>​ 
 +chem/​NAMD/<​version_string>​ 
 +</​code>​ 
 + 
 +Here, the ''<​version_string>''​ may deviate between the clusters. If you are missing a particular version, please inform us. 
 + 
 +<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. Subsequentlysend 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)
 </​WRAP>​ </​WRAP>​
  
-NAMD, recipient ​of a 2002 Gordon Bell Awardis a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systemsNAMD is file-compatible with AMBERCHARMM, and X-PLOR and is distributed free of charge with source ​code. +===== Using VMD ===== 
-Documentation ​and source ​code on the web page of "[[http://​www.ks.uiuc.edu/​Research/namd/|Theoretical and computational biophysics group]]"+ 
 +<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 GUIall 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) ==== 
 + 
 +Herewe give some brief snippetscovering 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:
  
-There are few possibilities to start NAMD simulation on the MOGON cluster.+<code bash> 
 +#!/bin/bash
  
-//<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>//+#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>
  
-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]].+module purge
  
-=== Memory Usage ===+module load chem/NAMD
  
-NAMD has traditionally used less than 100MB of memory even for systems +# the suffix '​namd_conf'​ is arbitrary 
-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.+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