Hi,
In the GROMOS force fields the non-bonded interactions are explicitly
given as some atom types have more than one C12 value. The different C12
values are used for interactions with different atom types. This means
you need to be very careful when modifying the ffnonbonded.itp for the
GROMOS force fields. If you wish to do this I suggest that you read of
the GROMOS 53A6 force field paper (DOI: 10.1002/jcc.20090).
Cheers
Tom
On 04/01/12 06:18, Mark Abraham wrote:
On 4/01/2012 4:43 PM, XUEMING TANG wrote:
Hello
I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon)
and also in Gromos (C6 and C12) forcefield for comparison. The
original ffnonbonded.itp file in oplsaa.ff has no pair potential
listed. While the original ffnonbonded.itp file in gromos**.ff listed
all the pair potentials. If I change one atom potential, do I need to
do anything to generate the new pair potential before running a
simulation in opls-aa force field? Or how to generate the pair
potentials? While for the case of gromos forcefield, the
forcefield.itp file shows no pair potential will be generated. Is
there any automatic ways to generate the modified LJ potentials?
Should I list every possible LJ pair potentials in nonbonded.itp file?
It looks like some very tedious work if several atoms are going to be
modified.
Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file?
Values of those two are different for OPLS and Gromos.
In general, two force fields work differently and have their own
idiosyncrasies that will show up in how GROMACS implements them. When
modifying them, you should be sure to check the original literature and
the GROMACS manual and satisfy yourself how your changes will work. You
should search the manual for discussion of the use of gen-pairs and the
fudge values. I don't know why the list of [ nonbond_param ] values is
exhaustive - you'd think the combination rules could be used. In
practice, you only need to add parameters for interactions that can
occur in your system, and grompp will complain about those that it can't
find.
Mark
--
Dr Thomas Piggot
University of Southampton, UK.
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