[gmx-users] last line in .gro file

[Erik Marklund]

Hi,

Since any unit cell can be formulated as a triclinic cell, the 
monoclinic cell is indeed supported. By definition it has two 90 degree 
angles and one that is not 90 degrees.  The box vectors can be of 
different lengths. You'll have to do the math and reading yourself to 
find out how this translates to a .gro box. The manual is your friend here.

Good luck,

Erik

Vishal Agarwal skrev:
> 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.
>
> 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


-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys