[gmx-users] Fwd: Adding new atom types

Alex alexanderwien2k at gmail.com
Thu Sep 6 16:28:31 CEST 2018

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!


---------- 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*

*Adding "OC24    8       15.99940        0.000000        A
      0.0035644156892674973      6.222504156102231e-06" to
the ffnonbonded.itp/[ atomtypes ]*

*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 ]


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