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.pig...@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 <alexanderwie...@gmail.com>
Date: Tue, Sep 4, 2018 at 2:43 PM
Subject: Adding new atom types
To: <gmx-us...@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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