[gmx-users] last line in .gro file

[Justin A. Lemkul]

Vishal Agarwal wrote:
> Dear Justin,
> 
> I am trying to set up calculations for a cellulose structure. The 
> allomorph of cellulose which I want to study has a monoclinic structure. 
> I have a .cif file of the XRD structure. I think the better question to 
> ask is how can I make input files using that.
> 

That is a far more complex question.  There are numerous posts in the list 
archive regarding preparing input for polymeric systems, so please do search the 
list archive.  I helped one user set up a polyethylene system some time ago, so 
that may help out.  You'll have to familiarize yourself with .rtp entry 
construction, specbond.dat (maybe), and the ins and outs of pdb2gmx to get it to 
work though.  There are lots of resources in the manual and on the Gromacs wiki 
pages to get you started.

-Justin

> thanks
> vishal
> 
> On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <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 <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

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