[gmx-users] last line in .gro file
Vishal Agarwal
vishal.iitian at gmail.com
Tue Feb 2 20:59:24 CET 2010
Dear Justin,
Thanks for replying. You mentioned that gromacs supports triclinic
structure. Can you tell me what will be the box parameters for triclinic
structure of cell parameters a, b, c and angles alpha, beta and gama.
Thanks in advance
Vishal
On Tue, Feb 2, 2010 at 12:30 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>> <mailto:gmx-users at gromacs.org>
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>>
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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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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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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