Thank you. Another question... I specify in my table functions e.g. g(x) and h(x) and it is written that I need to setup parameters C6 and C12. But where I should specify them? In :
[ atomtypes ] ;name at.num mass charge ptype V(c6) W(c12) O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06 or [ nonbond_params ] ; i j func V(c6) W(c12) O O 1 0.22617E-02 0.74158E-06 O OA 1 0.22617E-02 0.13807E-05 Or maybe both? On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/7/13 7:36 AM, Steven Neumann wrote: > >> Thank you, just getting into this. I just dont understand why they start >> from x=0.04? Why not 0.02 or sth else? >> >> > You can start the table from whatever value of x that you like, but at a > certain point, it is unlikely that particles ever come that close, given > normal repulsive potentials. > > -Justin > > > On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena >> <maruthi.s...@gmail.com>wrote: >> >> Hi Neumann, >>> You can use tabulated potential option in >>> gromacs. Please check the site given below: >>> >>> http://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials<http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials> >>> >>> Thanks, >>> Mohan >>> >>> >>> On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann <s.neuman...@gmail.com >>> >>>> wrote: >>>> >>> >>> Dear Gmx Users, >>>> >>>> I want to specify a table to mdrun for non bonded parameters. I wish to >>>> >>> set >>> >>>> it up for all atoms with same potential. Is there any example of the >>>> >>> table >>> >>>> like this? I want use my specific potential so table should have two >>>> columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right? >>>> How can I tell gromacs to use it for all interactions? >>>> >>>> Thanks >>>> >>>> Steven >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
