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

[Justin A. Lemkul]

darrellk at ece.ubc.ca wrote:
> 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.
> 

Right; if you have explicit definitions of bonds in the .top, those will 
override the defaults in the force field, IIRC.

> 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.

The terminology for OPLS is a little bizarre.  The opls_145 definition is used 
for nonbonded parameters; in the ffoplsaanb.itp file these atom types are 
translated into those used for bonded parameters, i.e.:

opls_145   CA  6     12.01100    -0.115       A    3.55000e-01  2.92880e-01

So a bond between two of these atoms would be defined using:

CA    CA      1    0.14000   392459.2   ; TRP,TYR,PHE

Thus, as long as the atom types have bonded interactions defined, it is 
sufficient to define:

[ bonds ]
1   2   1

in the topology.

-Justin

> 
> 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.
> 
> Darrell
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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