[gmx-users] last line in .gro file

[Vishal Agarwal]

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.

thanks
vishal

On Tue, Feb 2, 2010 at 11:52 AM, Justin A. Lemkul <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>> 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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-- 
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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