[gmx-users] last line in .gro file

[Justin A. Lemkul]

Vishal Agarwal wrote:
> Dear Justin,
> 
> Thanks for replying. The table mentions only a few unit cell type. I am 
> using a monclinic unit cell. Do you know how these box vectors have been 
> derived.
> 

Are you talking about your unit cell type, or the structure of the species you 
wish to simulate?  I see no mention of monoclinic box support in Gromacs, nor is 
it listed as a type of box that can be defined with editconf, so you need to 
clarify what it is you're trying to do.  In any case, the last line of the .gro 
file corresponds to the box vectors of the unit cell you specify with editconf. 
  If you don't specify anything explicitly, the default is to build a triclinic 
unit cell.

-Justin

> thanks
> vishal
> 
> On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Vishal Agarwal wrote:
> 
>         Dear gmx-users,
> 
>         I am new to GROMACS. Can anyone tell me what does the last line
>         in .gro file stands for ?
> 
>         The manual mentions
>         "box[X][X],box[Y][Y],box[Z][Z],
>         box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]"
> 
>         Can anyone explain what each of these mean in terms of cell
>         parameters ?
> 
> 
>     The last line contains the box vectors.  Specifics in terms of unit
>     cell geometry are given in the manual, Table 3.1 and section 3.2.1.
> 
>     -Justin
> 
>         Thanks,
>         vishal
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> -- 
> Regards
> 
> ***********************************************
> Vishal Agarwal
> Research Scholar
> University of Massachusetts, Amherst
> ***********************************************
> 'Your only obligation in any lifetime is to be true to yourself."
>             ---Richard Bach

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================