[gmx-users] Nonbonded parameters

Wed Jun 12 13:55:19 CEST 2013

"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.abraham at 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.neumann08 at gmail.com
> >wrote:
>
> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <mark.j.abraham at 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.neumann08 at 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.neumann08 at gmail.com
> > > > >wrote:
> > > >
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <jalemkul at 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 <jalemkul at 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 at 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-request at 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 at 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-request at 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 at 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-request at gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > --
> > > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>