[gmx-users] Optimization of the box size during an energy minimization?

[Justin A. Lemkul]

MyLinkka wrote:
> Hi Justin,
> 
> Thanks for your answer!
> 
> As far as I understood, the virial expression of pressure has two parts,
> the kinetic energy contribution and the potential energy contribution. 
> Even when
> temperature is undefined or zero, the product of pair force and distance 
> between
> atoms still contribute to the microscopic pressure tensor. In the EM 
> algorithm,
> if this pressure tensor is included in the target function to be 
> minimized, it should
> be able to optimize the box size as well as the atom positions, because 
> the pressure
> tensor is a functional of box size.
> 
> However, it's good to know that Gromacs is not doing this task. Thanks!
> 

I suppose, in theory, it's possible to use an EM algorithm to optimize a box. 
But for most systems, like a box filled with solvent, during EM the positions 
move very little and I'd be willing to bet the box wouldn't even change.  I 
guess it depends on what you're looking to do, but for a system that hasn't even 
been equilibrated under the desired thermodynamic conditions (with a proper 
velocity distribution applied to the atoms), I don't see any real value in 
trying to obtain what you might consider an "optimized" box for a system that is 
not at equilibrium.  The box stabilizes during NPT equilibration.

-Justin

> Ting Li
> 
> 
> On 12/25/2010 3:41 PM, Justin A. Lemkul wrote:
>>
>>
>> MyLinkka wrote:
>>>   Yeah! Energy minimization with pressure coupling.
>>> Is this possible?
>>>
>>
>> No.  There are no velocities in EM, and hence no kinetic energy, no 
>> virial, and thus no pressure coupling.
>>
>> -Justin
>>
>>> Ting
>>>
>>>
>>> On 12/24/2010 5:04 AM, Terry wrote:
>>>>
>>>>
>>>> On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham 
>>>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>>>
>>>>     On 24/12/2010 5:17 AM, MyLinkka wrote:
>>>>>
>>>>>
>>>>>           Does anybody know if it is possible to optimize the box
>>>>>           size during an energy minimization in Gromacs?
>>>>>
>>>>
>>>>     Optimize for what criterion?
>>>>
>>>>
>>>>>     Can I make pressure coupling if it's possible?
>>>>
>>>>
>>>> Do you mean  energy minimization with pressure coupling?
>>>>
>>>> Terry
>>>>
>>>>
>>>>     Sure, that's in the manual and covered in tutorials.
>>>>
>>>>     Mark
>>>>
>>>>
>>>>>     Is there a workaround if there is no direct way?
>>>>>
>>>>>     Thanks!
>>>>>
>>>>>     Ting
>>>>
>>>>
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>>>
>>
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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