Ahmed - This is *YOUR* research, not mine. I believe I have given you enough hints to succeed.
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 12:51 PM, ahmed sta <ahmedsta6...@yahoo.fr> wrote: > Can you help me please > > > Thanks for all > > ________________________________ > 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 17h33 > Objet : Re: Re : Re : Re : Gromacs > > 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
