An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4 combinations so it should be lower than 1800... And why 1830 1-4 interactions as I have only 57... Please, help/
Steven On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann <s.neuman...@gmail.com>wrote: > 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 <s.neuman...@gmail.com>wrote: > >> >> >> >> On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <jalem...@vt.edu> 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 <jalem...@vt.edu> >>>> 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 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