[gmx-users] Nonbonded parameters

Wed Jun 12 14:01:31 CEST 2013

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.abraham at gmail.com>wrote:

> How many atom *types* are there?
>
>
> On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann <s.neumann08 at 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.neumann08 at 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.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>
> > >> > > > >>>> >
> > >> > > > >>>>
> > >> > > > >>>> ==============================****==========
> > >> > > > >>>>
> > >> > > > >>>> --
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> > >> > > > >> --
> > >> > > > >> ==============================**==========
> > >> > > > >>
> > >> > > > >> 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>
> > >> > > > >>
> > >> > > > >> ==============================**==========
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