[gmx-users] Fwd: Adding new atom types

[Thomas Piggot]

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.