It is stated in manual that tables must always contain 7 columns with a meaningful data (i.e. no zeros). must be entered in all columns. The example of table6-12.xvg involves xeros until 0.04. How come? I want to cut my potential at some point to zero - can I put zeros or shall I specify some values so the potential will equal zero?
On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > > > > 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
