60 types of atoms and 60 atoms in total belonging to one residue
On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > How many atom *types* are there? > > > On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann <s.neuman...@gmail.com > >wrote: > > > and 1830 1-4 interactions... there are "57 all possible 1-4 interactions" > > > > > > On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann <s.neuman...@gmail.com > > >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 < > mark.j.abra...@gmail.com > > >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 < > s.neuman...@gmail.com > > >> >wrote: > > >> > > >> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham < > > >> mark.j.abra...@gmail.com > > >> > >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 < > > >> 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. 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Read 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 > -- 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