[gmx-users] dihedral potential

Mark Abraham Mark.Abraham at anu.edu.au
Sat Dec 20 05:01:29 CET 2008

manel.canales at upc.edu 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.


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