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

[MyLinkka]

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!

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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>>
>