[email protected] wrote:
Dear friends
I'm very new in the gromacs world, and I have a very basic question: I'm
interested to make simulations of polyaniline but using dihedral angle
Do you mean polyalanine?
parameters different from those collected in the ffG53a6bon.itp bonded
file force field. In this file the dihedral angle is always 180. However
the model that I would use says that the angle
is 163.
A properly parameterized model will say more than that, and you need to
include all the information you have. Ad hoc changes to and combinations
of forcefields are not normally defensible.
The formula 4.60 (page 54 of version 3.3 of the gromacs manual)
says:
V = k*(1+cos(n*fi-fi0))
Therefore a fast solution could be to modify the ffG53a6bon.itp file
replacing the fi0 =180 by the fi0 = 163. However I?m not really sure
because I have read the paper where
this force field appears and in te paper fi0 is 180. If this is the case
then ¿ I should solve the problem introducing dihedral harmonic
restraints (formula 4.69 and 4.70 of the manual) ?
That also moves your model of physics from something that might be
defensible to something that may not be known to be such.
Mark
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