[gmx-users] octahedron box (fwd)

[Anton Feenstra]

> From: Simon Wang <sim_wang03 at hotmail.com>
> To: spoel at xray.bmc.uu.se
> Subject: octahedron box
> 
> Hi, Dr. David van der Spoel:
> 
> How are you. I currently am using GROMACS 3.1.4 to set up some membrane 
> lipid simulation. The problem I have is to build the octadron box. The box 
> is always viewed like a rectangular box. I searched the mailing list archive 
> and found your suggestion to use 'trjconv -ur compact'. Apparently it still 
> doesn't work for my case. Your valuable suggestions will be highly 
> appreciated.

I am not sure if your problem concerns *building* an octahedral box or
*viewing* it. In the first case, building, it is quite simple: you can
build a rectangular box of the proper shape and 'tile' that in three
dimensions to get a space filled for a octahedral box. That is how, e.g.,
the editconf and genbox also treat octahedral (and dodecahedral) boxes.

In the second case, viewing, 'trjconv -ur compact' should help you out.

In any case, please describe exactly what you did, what you expected
and what happened so we can help you further...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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