I see, thanks Mark,
Best regards On Wed, Oct 11, 2017 at 3:46 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > To reproduce the training data for each forcefield, e.g. some experimental > or other computational result, e.g. the density of argon gas under various > conditions. Details of what and how do vary with the force field, are are > documented in its literature, of course. > > Mark > > On Wed, Oct 11, 2017 at 3:43 PM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > >> Apart from my own simulation, I do no understand how the values of C6 and >> C12 are obtained for each atoms in ''atometypes'' in force fields, could >> you tell me? >> >> >> Best regards >> >> >> On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett <w.barn...@columbia.edu> >> wrote: >> >>> >>> >>> On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh <fpoosa...@gmail.com> >>> wrote: >>> >>>> Thank you Wes and Mark, >>>> >>>> Wes, that is what I am trying to do. However, still have problem. >>>> I do not know how to derive sigma, epsilon (or C6 and C12) for my >>>> particle? >>>> How the force fields have obtained C6 and C12 values in their .itp >>>> files for each atom? >>>> >>> >>> That depends on what the purpose of your simulation is. If you're just >>> wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units >>> could be reasonable. >>> >>> >>>> >>>> >>>> Best regards >>>> >>>> >>>> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett <w.barn...@columbia.edu> >>>> wrote: >>>> >>>>> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com> >>>>> wrote: >>>>> >>>>> > Hi Mark >>>>> > >>>>> > I have a given function for pseudo hard-sphere potential, which has >>>>> > different powers than LJ and a constant. I have to insert the >>>>> constant in >>>>> > order to properly define the cut-off for my hard spheres. >>>>> > I just realized that I can use "user-specified potential". I guess I >>>>> can >>>>> > include the constant there, yes? >>>>> > >>>>> > One more thing, I need to have my own particles, spheres with a >>>>> diameter >>>>> > "a". How can I have them in gromacs? >>>>> > . >>>>> > >>>>> >>>>> This should get you started in generating your own tables: >>>>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials >>>>> >>>>> If all you're looking to do is create repulsive spheres (again, not >>>>> true >>>>> hard spheres as Mark said; just removing attractions from the >>>>> interactions), then cut off your interactions at 2^(1/6)*sigma and >>>>> shift >>>>> the potential at the cutoff to zero in your table. If you want >>>>> different >>>>> size spheres you need to subtract an additional term from r in the >>>>> denominators of the c6 and c12 terms. >>>>> >>>>> -- >>>>> James "Wes" Barnett >>>>> Postdoctoral Research Scientist >>>>> Department of Chemical Engineering >>>>> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> >>>>> Columbia University >>>>> w.barn...@columbia.edu >>>>> http://wbarnett.us >>>>> -- >>>>> 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. >>>>> >>>> >>>> >>> >>> >>> -- >>> James "Wes" Barnett >>> Postdoctoral Research Scientist >>> Department of Chemical Engineering >>> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> >>> Columbia University >>> w.barn...@columbia.edu >>> http://wbarnett.us >>> >> >> -- 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.