[Openmd-users] OpenMD stuntDoubles and visualizing the result

[Dan Gezelter]

> 
> 	• In StuntDouble by using pv or pvqj we can define the position of each atom. As I feel it is very much difficult to hand written position of each atom. Is there any software for this. cant we do this work using PackMole.

There are a few utilities bundled with OpenMD that can be used to build specific structures:

   simpleBuilder       - builds a simple fcc lattice at a specified density
   randomBuilder       - builds a simple fcc lattice with multiple components 
   waterBoxer          - builds a lattice of water molecules in a periodic box
   nanoparticleBuilder - builds spherical fcc nanoparticles
   nanorodBuilder      - builds spherically-capped cylinders or ellipsoids
   icosahedralBuilder  - builds various icosahedra and decahedral structures
   nanorod_pentBuilder - builds pentagonal twinned-lattice nanorods

All of these programs are built and installed with OpenMD, and if you use the "-h" flag, you'll get a list of the parameters that they accept.

If you built OpenMD with the openbabel library, the build should have created another program that can be useful in converting from xyz, pdb or many other formats into a rough md file:

   atom2md -ixyz file.xyz 

will create an incomplete OpenMD file called file.md  with guesses at atom types.  Most of the files converted using atom2md will need significant editing, but it does  save an immense amount of work.

> 	• I also confused with the guidelines at the internet. "http://openmd.org/?cat=4"  Building and equilibrating a gold nanooparticle in OpenMD steps from 2 to down. from where do we have to call these commands

All of these programs should be installed in the same directory as openmd.  When you call these commands, you should working in the same directory as the input files you are using.


> 	• finally I had a problem in Installing the software after running the command "make", It gives me error after installing  97%

Can you forward the error messages you got?  It is hard to diagnose a problem without the error message.

Best regards,

 --Dan Gezelter

***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
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