[gmx-users] eelctric field

[Christian Blau]

Hi Amin,


Sorry for the late answer - when calculating the pressure, no information about the electric field is used (as it should 
be). To obtain the pressure as if no electric field were applied, running another simulation with the field switched off 
is the only way.


Best,

Christian

On 11/15/19 3:20 PM, Amin Rouy wrote:
> Dear Christian,
>
> Thank you for the answer.  My last question I hope:
>
> I just noticed that the pressure I get in y and z directions seem physical
> and correct, but the x direction of pressure is a big negative number and
> not reasonable (Pres-ZZ = -400 bar). (I had applied the filed in x
> direction and I have NVT ensemble). So I think the way Gromacs calculates
> the pressure in presence applied field does not take into account the field
> effect, am I correct?
>
> On Fri, Nov 15, 2019 at 11:17 AM Christian Blau <blau at kth.se> wrote:
>
>> Hello Amin,
>>
>>
>> Though the forces are present during the simulation the additional work on
>> the system that is exerted via the electric
>> field is not output as an additional energy term in GROMACS.
>>
>> I believe the pressure deviations that you observe are due to two
>> different effects:
>>
>>       - the pressure fluctuates much more than energies, like coulomb
>> interactions, etc., especially in small systems.
>> The question here would be if the deviation between the perturbed and
>> unperturbed system that you observe is larger than
>> the deviation between two unperturbed systems
>>
>>       - the electric field indirectly influences the pressure. I would
>> expect this effect to be usually small, but if you
>> imagine a system consisting only of the same number of positively and
>> negatively charged ions, applying the electric
>> field along z-direction will cause half of them to move upwards and the
>> other half downwards along the z-direction,
>> which will in turn affect the pressure.
>>
>>
>> Best,
>>
>> Christian
>>
>> On 11/13/19 3:39 PM, Amin Rouy wrote:
>>> Dear Christian,
>>>
>>> Thank you for your reply. However, still it is not fully clear to me.
>> Lets
>>> only talk about gmx energy.  How it happens that I get from gmx energy
>>> similar values of energies (LJ, columbs, total energies) while a
>> different
>>> pressure, with and without applied filed? The total energy should be
>>> different as a result of an additional energy due to applied filed on
>> each
>>> atom.
>>>
>>> On Wed, Nov 13, 2019 at 3:10 PM Christian Blau <blau at kth.se> wrote:
>>>
>>>> Hello Amin,
>>>>
>>>>
>>>> When you apply an electric field during the simulation by setting the
>> mdp
>>>> parameters like E-x =... as you describe,
>>>> nothing more happens than that each atom experiences an additional force
>>>> that is "atom charge * field strength". The
>>>> energy terms or virial (that then would relate to pressure coupling) are
>>>> not influenced by this. If these terms differ
>>>> between a simulation with electric field and one without, then only
>>>> because the system as a whole responds to the
>>>> applied electric field.
>>>>
>>>> gmx potential on the other hand is an analysis tool that is per se
>>>> unrelated on how you chose to apply an electric field
>>>> during your simulation or not. However, when applying an electric field,
>>>> you would expect a different result from an
>>>> analysis with gmx potential than without electric field, because your
>>>> system will respond to the applied electric field.
>>>>
>>>>
>>>> Best,
>>>>
>>>> Christian
>>>>
>>>> On 11/13/19 2:44 PM, Amin Rouy wrote:
>>>>> Hi,
>>>>>
>>>>> I am using gromacs 5.0.4. I apply a uniform electric field in x
>> direction
>>>>> of my box (no walls),
>>>>> E-x= 1  10  0, and simulation runs without error.
>>>>> I notice that the values of electrostatic interactions I get from the
>>>>> simulation is the same as without the an electric field. Which is
>>>> strange,
>>>>> but according to previous questions in the gromacs forum this is true:
>>>>> ''gmx potential only calculates the electric field and potential of the
>>>>> system. It does not take into account the applied field.''
>>>>>
>>>>> Now, my question is are the other quantities obtaining from gmx energy
>>>> take
>>>>> into account field effect? e.g. pressure of the system.
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