How many atom *types* are there?
On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann <[email protected]>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 <[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 > -- 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
