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

Erik Marklund Tue, 02 Feb 2010 12:24:14 -0800

Hi,

Since any unit cell can be formulated as a triclinic cell, themonoclinic cell is indeed supported. By definition it has two 90 degreeangles and one that is not 90 degrees. The box vectors can be ofdifferent lengths. You'll have to do the math and reading yourself tofind 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. Iam using a monclinic unit cell. Do you know how these box vectors havebeen derived.


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



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Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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