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

[Dr. Vitaly V. Chaban]

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



-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA