I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp:
Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1 Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1 Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <[email protected]>wrote: > > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <[email protected]> wrote: > >> >> >> On 6/12/13 6:00 AM, Steven Neumann wrote: >> >>> Thank you. That means that e.g. when two LJ atoms of a different type >>> approaching each other the non bonded LJ potential energy is a sum of two >>> potentials of those atoms? >>> >>> >> No, please refer to the Gromacs manual for discussion on "combination >> rules" and how they fit into the Lennard-Jones equation. >> >> -Justin >> > > I read it. > I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that > means that when you provide in [atomtypes] in ffnonbonded your C and A > values each atom has a specific LJ potential shape. Right? > So two of them approaching each other in my system will have have the sum > of it. > > Steven > > > >> >> >>> On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <[email protected]> wrote: >>> >>> >>>> >>>> On 6/12/13 5:30 AM, Steven Neumann wrote: >>>> >>>> Dear Gmx Users, >>>>> >>>>> Please, correct me if I am wrong. In ffnonbonded.itp >>>>> >>>>> [ atomtypes ] - these are nonbonded parameters between atoms of the >>>>> same >>>>> type >>>>> >>>>> >>>> No, these are the nonbonded parameters that are used when applying >>>> combination rules between any atoms. >>>> >>>> >>>> [ nonbond_params ] these are nonbonded parameters between atoms of >>>> >>>>> different type >>>>> >>>>> >>>> No, these override combination rules. >>>> >>>> >>>> [ pairtypes ] - 1-4 interactions >>>> >>>>> >>>>> If that is correct why amber force filed has only [atomtypes] column? >>>>> How >>>>> nonbonded parameters are calculated between atoms of a different type? >>>>> The same with charmm - only [atomtypes ] and [pairtypes ] are provided. >>>>> Would you please explain? >>>>> >>>>> >>>>> Gromos force fields, for instance, have complex ways of generating >>>> nonbonded interactions that are not always the same for a given >>>> atomtype. >>>> Other force fields just use straight combination rules and thus never >>>> need >>>> [nonbond_params]. >>>> >>>> -Justin >>>> >>>> -- >>>> ==============================****========== >>>> >>>> >>>> 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 [email protected] >>>> 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 [email protected]. >>>> * 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 [email protected] >> 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 [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
