On Fri, Jul 29, 2011 at 12:14 PM, Alex Marshall <amars...@uwo.ca> wrote:
> 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. Why not use 0 for LJ parameters? You will have to figure out the units of energy and force in the reference otherwise you cannot make the comparison. > > > 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 >
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