[gmx-users] Fwd: Adding new atom types

[Thomas Piggot]

I'm not sure off the top of my head. The manual says:

"Pair parameters that are not present in the [ pairtypes ] section are 
only generated when gen-pairs is set to “yes” in the [ defaults ] 
directive of forcefield.itp"

so it sounds like the parameters in the [ pairtypes ] section should be 
kept if they are there. You could check this easily yourself by running 
a simple test case through grompp and seeing what is done.

However, I should clarify/correct what I was wrote in my previous 
message as it wasn't 100 % correct (it's been a long week already!).

Rather than [ nonbonded_params ] and [ pairtypes ] sections, I was 
actually referring to the link between the values given in the [ 
atomtypes ] and [ nonbonded_params ] sections of the GROMOS 
ffnonbonded.itp files. So this is where there are up to 3 different C12 
values used to calculate the nonbonded_params for some atomtypes, as 
defined in the two tables I mentioned before in the linked paper. 
Because of the different C12 values, this is why you can't predict the [ 
nonbonded_params ] from the [ atomtypes ] using the standard combination 
rules.

For the [ pairtypes ], you also can't predict some of these from the [ 
nonbonded_params ] sections (using fudgeLJ) because some of the 
atomtypes have explicit C6/C12 values to use just for 1-4 interactions 
(as given in table 9 of the paper I linked to), while others follow the 
fudgeLJ rule (i.e. are the same as those given in the [ nonbonded_params 
] section). Because of this, you shouldn't try to generate the pairs for 
your new atomtype using gen-pairs but you should manually calculate and 
add them (as well as doing the same for the values in the [ 
nonbonded_params ] section). You should also be careful in doing these 
calculations because the C12 values given in the [ atomtypes ] section 
might not be the ones you want to use in the calculation of the 
nonbonded_params values for your new atomtype (even if your new atomtype 
only has one C12 value). That's because some of the atomtypes interact 
with themselves using the type 2 C12 values (e.g. atomtype OA), and so 
these are the values given for C12 in the [ atomtypes ] section

Hopefully that all makes sense.

Cheers

Tom

On 06/09/18 18:42, Alex wrote:
> 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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-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.