Sure, possible. But if you want to type the coordinates for FCC lattice using 500 atoms by hand, that's indeed cool.
On Fri, May 25, 2012 at 11:31 AM, ahmed sta <ahmedsta6...@yahoo.fr> wrote: > I thought that it is possible to use text editor in order to fix the > geometry, isn't it? > > > ________________________________ > De : Dr. Vitaly V. Chaban <vvcha...@gmail.com> > À : ahmed sta <ahmedsta6...@yahoo.fr> > Cc : gmx-users@gromacs.org > Envoyé le : Vendredi 25 mai 2012 18h15 > Objet : Re: Re : Re : Gromacs > > Writing your program has nothing to do with gromacs. If you do not > have experience in programming by far, it may be faster to use the > second route. But of you still want to generate a program yourself, I > am delighted to direct your attention to the PYTHON, python.org, > programming language. > > I am aware of some commercial software like MedeA and (perhaps?) > Materials Studio, capable to generate molecular configurations of > various symmetries. Maybe, someone in the gromacs mailing list can > suggest a free alternative as well. > > > > On Fri, May 25, 2012 at 11:05 AM, ahmed sta <ahmedsta6...@yahoo.fr> wrote: >> Well i see >> >> I think that writing my own program would be better and more accurate >> How should i proceed ? >> it is my first use of Gromacs and i do not know how to do >> >> Regards >> >> ________________________________ >> De : Dr. Vitaly V. Chaban <vvcha...@gmail.com> >> À : ahmed sta <ahmedsta6...@yahoo.fr> >> Cc : gmx-users@gromacs.org >> Envoyé le : Vendredi 25 mai 2012 17h58 >> Objet : Re: Re : Gromacs >> >> If you want a solid system, where atoms are arranged as in FCC, this >> is another talk. >> >> There two way to achieve your goal. Either -- >> >> 1) you write a simple program which places argon atoms as in FCC. >> >> OR >> >> 2) you try to freeze my system into your system using simulated >> annealing implemented in gromacs. Provided that argon is a pretty >> simple system, this should not take too much time. At least, I can say >> that our students get it (216 atoms) freezed during one laboratory >> work. >> >> BTW, there is no guarantee that the freezing point of the classical >> argon model is perfectly reproduced. My guess is based on the fact >> that the density of the liquid phase (in the NPT ensemble) is not >> ideal. >> >> >> Dr. Vitaly V. Chaban, 430 Hutchison Hall >> Dept. Chemistry, University of Rochester >> 120 Trustee Road, Rochester, NY 14627-0216 >> THE UNITED STATES OF AMERICA >> >> >> >> On Fri, May 25, 2012 at 10:44 AM, ahmed sta <ahmedsta6...@yahoo.fr> wrote: >>> Sorry. My aim is to model FCC Argon (not liquid state) and i am trying to >>> define that geometry >>> Can you help me please? >>> >>> Regards >>> >>> ________________________________ >>> De : Dr. Vitaly V. Chaban <vvcha...@gmail.com> >>> À : ahmed sta <ahmedsta6...@yahoo.fr> >>> Cc : gmx-users@gromacs.org >>> Envoyé le : Vendredi 25 mai 2012 17h36 >>> Objet : Re: Gromacs >>> >>> Dear Ahmed - >>> >>> I do not understand how you imagine "FCC geometry" in the liquid state >>> of matter. >>> >>> If you want to just resize my system, use the standard "genbox" >>> utility and then re-equilibrate at the desired temperature and density >>> (if you want to fix density, of course). >>> >>> >>> Dr. Vitaly V. Chaban, 430 Hutchison Hall >>> Dept. Chemistry, University of Rochester >>> 120 Trustee Road, Rochester, NY 14627-0216 >>> THE UNITED STATES OF AMERICA >>> >>> >>> >>> On Fri, May 25, 2012 at 10:30 AM, ahmed sta <ahmedsta6...@yahoo.fr> >>> wrote: >>>> Dear Vitaly >>>> >>>> >>>> I am an engineer student and i am now trying to use Gromacs >>>> I found your Argon molecule defined topology created in May 2009 >>>> I want to ask you how to define my own geometry on Gromacs >>>> In fact i am trying to define liquid Argon system with a density >>>> equilibrated at 90K. My system should have a FCC geometry and containing >>>> for >>>> example 500 atoms >>>> >>>> >>>> I really need your help >>>> >>>> Best regards >>>> >>>> >>>> >>>> >>>> Ahmed Sta >>>> Ensta Paristech engineering school >>>> ahmedsta6...@yahoo.fr >>> >>> >> >> > > -- Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists