I'm trying to calculate the total electrostatic energy of the system, and the force in the Z direction on the particle placed above the lattice. It's a purely electrostatic problem, ideally LJ shouldn't come into it at all, but I don't know how else to convert the resulting energy and force to dimensionless units, which I must do because I was given reference values in dimensionless units.
I guess I'm not actually using gmx.ff, I was just using the C6-C12 convention for LJ parameters used in that forcefield's ffnonbonded.itp. On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey <kgp.a...@gmail.com> wrote: > I am not sure what you want to measure. You mentioned that "force and > energy I calculate are still quite far from the reference values", now are > you only looking at electrostatic contributions to these or the total > contributions? If its total contribution then LJ parameters should also be > correct and for that you should switch to standard gromacs units. > > Also why do you need to use gmx.ff, seems to me that you already have the > parameters (ie the LJ parameters and charges) > > > On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall <amars...@uwo.ca> wrote: > >> Hi Amit, >> >> So if I understand you correctly, any LJ interaction I impose on these >> particles will be quite arbitrary because I'm only concerned with >> electrostatics, right? How then might I go about comparing the dimensionless >> reference values given with the values I calculated? I don't think I can >> simply compare their ratios, as there would still be a unit of length to >> deal with. >> >> Thanks, >> Alex >> >> On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey <kgp.a...@gmail.com> wrote: >> >>> Hi, >>> >>> reduced units works for LJ particles only. I am not sure if it works when >>> you include electrostatics. When you set charge = 1 it is 1electronic >>> charge. I would suggest not to use the reduced units for LJ in this >>> scenario. >>> >>> Amit >>> >>> On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall <amars...@uwo.ca> wrote: >>> >>>> Hi all, >>>> >>>> I'm trying to calculate the force on one particle and the total >>>> electrostatic energy of my system, which consists of a lattice of 25 evenly >>>> spaced charges in the xy plane and a single charge in the center above to >>>> preserve charge neutrality. The reference values I have been given are in >>>> dimensionless units, so I am tasked with either converting my output to >>>> dimensionless units or having gromacs work in reduced units from the get >>>> go. >>>> I have set the mass of each charge to 1, the magnitude of the charge on >>>> each >>>> particle to 1, and the values of the C6 and C12 parameters in my itp file >>>> to >>>> 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. >>>> I've turned off temperature coupling because this is purely a test of the >>>> handling of electrostatics with 3D Ewald summation plus the correction for >>>> slab geometry. However, the force and energy I calculate are still quite >>>> far >>>> from the reference values. Have I missed anything if I want my output to be >>>> in dimensionless units? >>>> >>>> Thanks, >>>> Alex >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists