[gmx-users] Re: Re : Gromacs

[Dr. Vitaly V. Chaban]

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
>
>