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 <jalem...@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 <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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> 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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@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 >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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@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 interface > or send it to gmx-users-requ...@gromacs.org. > 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
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