and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann <[email protected]>wrote: > "All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 > from? > > > On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham > <[email protected]>wrote: > >> "Parameters for possible interactions" is not the same as "interactions." >> The latter depend on the configuration and cut-offs... grompp is not doing >> a neighbor search! >> >> Mark >> >> >> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann <[email protected] >> >wrote: >> >> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham < >> [email protected] >> > >wrote: >> > >> > > grompp is just enumerating the possible combinations of parameters >> given >> > > your inputs. Whether any of those will be used in the simulation will >> > > depend on whether atoms of given types are close enough and not >> excluded. >> > > >> > > Mark >> > >> > >> > I understand...but why for 60 mer polypeptide there are 1830 nonbonded >> > interactions ? >> > >> > > >> > > >> > > On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann < >> [email protected] >> > > >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 < >> > [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 >> > > > >> > > -- >> > > 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 >> > > >> > -- >> > 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 >> > >> -- >> 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 >> > > -- 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
