[gmx-users] Re: FCC lattice of argon

Dr. Vitaly V. Chaban vvchaban at gmail.com
Fri May 25 18:56:08 CEST 2012


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 <ahmedsta6600 at yahoo.fr> wrote:
> Can you help me please
>
>
> Thanks for all
>
> ________________________________
> 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 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 <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
>



More information about the gromacs.org_gmx-users mailing list