[gmx-users] Re: Re : Re : Gromacs

[Dr. Vitaly V. Chaban]

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 <ahmedsta6600 at 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 <vvchaban at gmail.com>
> À : ahmed sta <ahmedsta6600 at yahoo.fr>
> Cc : gmx-users at 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 <ahmedsta6600 at 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 <vvchaban at gmail.com>
>> À : ahmed sta <ahmedsta6600 at yahoo.fr>
>> Cc : gmx-users at 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 <ahmedsta6600 at 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
>>> ahmedsta6600 at yahoo.fr
>>
>>
>
>