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 <[email protected]> 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 <[email protected]> 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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