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

Justin A. Lemkul Tue, 02 Feb 2010 09:32:47 -0800


Vishal Agarwal wrote:

Dear Justin,
I am trying to set up calculations for a cellulose structure. Theallomorph 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 toask is how can I make input files using that.

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


-Justin

thanks
vishal

On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto: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> <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

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

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