[gmx-users] eelctric field

[Amin Rouy]

Dear  Christian,

Thank  you, I appreciate your help.

On Tue, Nov 19, 2019 at 11:59 AM Christian Blau <blau at kth.se> wrote:

> 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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> >> --
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