Hi, I tried using the regular PME method with and without corrections. The results don't depend on the choice of ewald-geometry at all!
I used (Gromacs 5.1): wall-ewald-zfac = 3 ewald-geometry = 3d ; This prompts a warning because I am using 2 walls - 2d system. I forced this with maxwarn. E-z = 1 5 0 and I also used wall-ewald-zfac = 3 ewald-geometry = 3dc ; No warnings since this is recommended E-z = 1 5 0 I checked that this input was being processing correctly on topol.tpr. For the first case, I see ewald-geometry = 0 and the second case ewald-geometry = 1. The electric field from ionic liquid has a magnitude of ~7.5 V/nm in the opposite direction to the applied electric field for both cases. This is greater than the applied 5. I obtained the electric field using gmx potential. I would very much appreciate any recommendations. Dan <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#m_-5936464299898835406_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Mon, Nov 13, 2017 at 10:22 AM, Dan Gil <dan.gil9...@gmail.com> wrote: > Hi, > > I am using gmx potential to measure the electric field. I've reported the > values from field.xvg in my previous email. The field at the edges of the > ionic liquid near the walls will oscillate because of the electric double > layer but it is the bulk field I am concerned with. > > I read the supporting information - I thought that the Ewald summation > correction for 2 dimensions was supposed to cancel out interactions between > periodic images in the z direction? > > Were you using the regular 3-D Ewald summation in this work? I might try > carrying out the calculations that way. > > Dan > > On Mon, Nov 13, 2017 at 2:23 AM, David van der Spoel <sp...@xray.bmc.uu.se > > wrote: > >> On 11/11/17 16:44, Dan Gil wrote: >> >>> Hi, >>> >>> Just wanted to see if anyone had any thoughts... >>> >>> For more information, if I use: >>> wall-ewald-zfac = 3 >>> E-z = 1 5 0 >>> The electric field from ionic liquid has a magnitude of 7.5 V/nm in the >>> opposite direction to the applied electric field. This makes no sense to >>> me >>> at all. >>> >>> With >>> wall-ewald-zfac = 5 >>> E-z = 1 5 0 >>> The ionic liquid E is -6.2 >>> >> How do you measure the electric field? Using gmx potential? >> What numbers does the (optional?) file field.xvg contain? >> >> There can of course be a difference between applied field and effective >> field, in particular with PBC. I sugges you read the supporting information >> for our paper: Carl Caleman and David van der Spoel: Picosecond Melting of >> Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed. >> 47 pp. 1417-1420 (2008) >> >>> >>> With >>> wall-ewald-zfac = 10 >>> E-z = 1 5 0 >>> The electric field is still slightly above the expected 5 V/nm. >>> >>> The dimensions of the box is about 5x5x20 nm3. >>> >>> Reading various sources say that the wall factor should not matter as >>> long >>> as it is sufficiently large (x3) but in my case it seems to matter a lot. >>> Should I report this as a bug or do you think I can investigate this >>> further? >>> >>> Best Regards, >>> >>> Dan >>> >>> <http://www.avg.com/email-signature?utm_medium=email&utm_sou >>> rce=link&utm_campaign=sig-email&utm_content=webmail> >>> Virus-free. >>> www.avg.com >>> <http://www.avg.com/email-signature?utm_medium=email&utm_sou >>> rce=link&utm_campaign=sig-email&utm_content=webmail> >>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >>> >>> >>> On Wed, Nov 8, 2017 at 11:37 AM, Dan Gil <dan.gil9...@gmail.com> wrote: >>> >>> Hello, >>>> >>>> I am studying room-temperature ionic liquids in slab geometry and I am >>>> experiencing that I cannot get rid of the interactions between periodic >>>> images in the z-direction. Is there something wrong with what I am >>>> doing or >>>> is this inevitable? >>>> >>>> The reason I think this is because when I change "wall-ewald-zfac" the >>>> results change also. >>>> >>>> Gromacs 5.1 >>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>>> - >>>> ;Integration Method and Parameters >>>> integrator = md >>>> nsteps = 4000000 >>>> dt = 0.002 >>>> nstenergy = 100 >>>> nstcalcenergy = 100 >>>> nstlog = 5000 >>>> >>>> ;Output Control >>>> nstxout = 100 >>>> nstvout = 10000000 >>>> >>>> ;Cutoff Schemes >>>> cutoff-scheme = verlet >>>> rlist = 1.0 >>>> vdw-type = cut-off >>>> rvdw = 1.0 >>>> DispCorr = EnerPres >>>> >>>> ;Coulomb interactions >>>> coulombtype = pme >>>> rcoulomb = 1.0 >>>> fourierspacing = 0.4 >>>> >>>> ;Constraints >>>> constraints = all-bonds >>>> >>>> ;Temperature coupling >>>> gen-vel = yes >>>> tcoupl = v-rescale >>>> tc-grps = System >>>> tau-t = 0 >>>> ref-t = 300 >>>> >>>> ;Walls >>>> pbc = xy >>>> nwall = 2 >>>> wall-type = 10-4 >>>> ewald-geometry = 3dc >>>> wall-atomtype = cp cm >>>> wall-density = 5 5 >>>> wall-ewald-zfac = 10 >>>> >>>> ;Electric Field >>>> ;Cosine with freq=0, Field V/nm, Phase=n/a >>>> E-z = 1 0 0 >>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>>> - >>>> >>>> Best Regards, >>>> >>>> Dan >>>> >>>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> 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.
