[gmx-users] eelctric field

[Amin Rouy]

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.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.