[gmx-users] How are bond parameters linked to atoms when using #include?

darrellk at ece.ubc.ca darrellk at ece.ubc.ca
Fri May 8 04:05:31 CEST 2009

Hi All,
I have just executed my first mdrun and it appears that the default bond
parameters from x2top were used instead of the bond parameters from the
oplsaa force field files which are included in my .top file.

Here is an extract from my .top file with the include statement:
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
ICE                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass 
typeB    chargeB      massB
     1   opls_145      1   Grph      C      1          0     12.011   ;
qtot 0
     2   opls_145      1   Grph      C      2          0     12.011   ;
qtot 0
     3   opls_145      1   Grph      C      3          0     12.011   ;
qtot 0

The .top file clearly shows that C is associated with opls_145.
Therefore, I would have thought that the bond parameters associated with
opls_145 would have been used in mdrun. Also, I tried to find opls_145
in ffoplsaabon.itp to see the bond parameters for opls_145 but I could
not find opls_145 in this file. Maybe I am confused and need some
direction as I do not seem to understand how GROMACS assigns bond
parameters to atoms in a structure.

Here is an extract from the grompp.log file that shows the default bond
parameter for kb (4.000000e+05) being used:
found directive 'bonds'
"graphene_nm_test.top" : 6428 : 1 2 1 1.420000e-01 4.000000e+05
1.420000e-01 4.000000e+05
push_bondnow: nr = 0
"graphene_nm_test.top" : 6429 : 1 3 1 1.420000e-01 4.000000e+05
1.420000e-01 4.000000e+05
push_bondnow: nr = 1

Thanks in advance for your assistance.


More information about the gromacs.org_gmx-users mailing list