Dear Christian, Thank you, I appreciate your help.
On Tue, Nov 19, 2019 at 11:59 AM Christian Blau <b...@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 <b...@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 <b...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.