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

[MyLinkka]

Agree! For most of the simulation of biological systems, EM with pressure coupling is
  not really necessary. However, it's maybe useful in some studies,such as the simulation of
a peptide crystal. Anyway, thanks for the answer! Happy new year!

Ting

On 12/29/2010 7:31 PM, Justin A. Lemkul wrote:
>
>
> 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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>>>>
>>>
>>
>>
>

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