Re: [gmx-users] last line in .gro file

Tue, 02 Feb 2010 08:53:53 -0800 


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 <jalem...@vt.edu 
<mailto:jalem...@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

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