[gmx-users] Nonbonded parameters

Wed Jun 12 13:45:45 CEST 2013

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

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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