[gmx-users] Fwd: Adding new atom types

[Alex]

Hi Tom,
Thanks for the informative response.

For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are
taken from the parameters existed [ pairtypes ], if I change the gen-pairs
to "yes" in Gromos FF, would you please confirm me that the parameters in [
pairtypes ] is still in privilege for those interactions whose parameters
EXIST in the [ pairtypes ]? And if the parameters are not there they will
be calculated by the fudgeLJ.

Regards,
Alex

On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot <t.piggot at soton.ac.uk> wrote:

> The GROMOS force fields are somewhat different to the others in that
> they provide specific 1-4 interactions by having several different C12
> parameters for one atomtype (in some cases). The C12 value used depends
> upon the atomtypes involved in the interactions (see tables 7 and 8 of
> https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more
> information for GROMOS 53A6). This means you cannot directly calculate
> the pairtypes from the nonbonded_params sections of the itp as you do
> not know what C12 value to use for the interaction.
>
> This also needs to be appropriately taken into account when adding a new
> atom type. You also need to explicitly add in the pairtypes, as by
> having multiple potential C12 parameters means it isn't possible to
> generate the pairtypes automatically.
>
> Cheers
>
> Tom
>
> On 06/09/18 15:27, Alex wrote:
> > Dear all,
> >
> > Any idea please about my both questions below?
> > The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the
> > combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule
> > about c12 in either sections!
> >
> > Thanks.
> > Alex
> >
> >
> > ---------- Forwarded message ---------
> > From: Alex <alexanderwien2k at gmail.com>
> > Date: Tue, Sep 4, 2018 at 2:43 PM
> > Subject: Adding new atom types
> > To: <gmx-users at gromacs.org>
> >
> >
> > Hi all,
> > Two questions on which your comments would be highly appreciated;
> >
> > 1. What is the difference between [ nonbond_params ] and [ pairtypes ]
> > sections in ffnonbonded.itp file?
> > For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have
> > similar numbers for an the similar interactions when it is counted as
> > [ nonbond_params
> > ] or as [ pairtypes ] because of the scale = 1, but the "OE OA"
> interaction
> > parameters change in  [ nonbond_params ] to [ pairtypes ], similar story
> > for the " OA O" interaction. Which is in contrast with my
> > understanding of "fudgeLJ
> > = 1".
> >
> >   [ nonbond_params ]
> > ;       i       j       func    c6              c12
> >
> > *        OE      OA      1       2.261954E-03    1.505529E-06*
> > *        OA      O       1       2.261954E-03    1.386510E-06*
> >
> > [ pairtypes ]
> > ;       i       j       func    c6              c12
> > *        OE      OA      1       2.261954E-03    1.265625E-06*
> > *        OA      O       1       2.261954E-03    9.687375E-07*
> >
> > 2. The gmx grompp gives some errors like;
> > ERROR 1 [file topol.top, line xxxx]
> >   No default LJ-14 types
> >
> > Which needs me to introduce new atom type ( of the problematic atoms)
> > in atomtypes.atp
> > and then in ffnonbonded.itp;
> > Would you please confirm the procedure I should take to do so;
> > First I have to add the atom type in atomtypes.atp: OC24 is an example;
> >
> > *echo "OC24 15.99940" >> atomtypes.atp*
> >
> > Then:
> > *Adding "OC24    8       15.99940        0.000000        A
> >        0.0035644156892674973      6.222504156102231e-06" to
> > the ffnonbonded.itp/[ atomtypes ]*
> >
> > Then:
> > *Adding the ";       i       j       func    c6      c12" for the OC24
> > in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]*
> >
> > Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and
> > ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or
> the [
> > nonbond_params ] and [ pairtypes ] can be descided/governed by normal
> > combination rule used in the FF, so that I do not need to put them in [
> > nonbond_params ] and ffnonbonded.itp/[ pairtypes ]
> >
> > Thanks.
> > Alex
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
> --
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