darre...@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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