On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 6/7/13 8:21 AM, Steven Neumann wrote: > >> 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? >> >> > Try the tutorial first and make sure you can replicate it. If you're just > looking to tweak C6 and C12 parameters, there's no need for tabulated > functions at all. > > -Justin > I want to change function g(x) to use Chandler Anderson potential so g(x) = 1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes] can I specify my my own C6 C12 ? > > >> 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> >>>>> <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> >>>>>> <htt**p://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> >>>>>> <h**ttp://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> >>>>>> <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> >>>>> <htt**p://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> >>>>> <h**ttp://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> >>>>> <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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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> >>> <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