[gmx-users] angle parameters in G96

[Erik Lindahl]

jxs818 at bham.ac.uk wrote:

>Hi All, 
>Just a quicky. I am trying to make a .rtp entry for a 
>ligand I am working on. I have a paper which describes the 
>angles within the ligand itself. I am working with ffG43a1 
>forcefield, My question is are the angle parameters used 
>in ffG43a1 in KJ/mol or KJ/mol/rad^2?? as the chapter on 
>topologies hurts my head ;-). My second question is a real 
>dumma, the parameters in the paper are in KJ/mol/rad^2 can 
>I use these numbers as is even though even if the angles 
>section of the .rtp file requires parameters in KJ/mol. 
>told you it was a dumma
>Cheers 
>John 
>  
>
Hi John,

We stick to SI units throughout Gromacs. This means the angle
parameters in the Gromos96 forcefields are in units of kJ/mol.

Gromos96 uses an angle definition like (type 2 in Gromacs)

V = 0.5 * k * (cos(theta)-cos(theta0))^2

In other words, there are no radian units in the force constant.

The alternative is the normal harmonic angle potential (type 1)

V = 0.5 * k (theta-theta0)^2

where the units of k are kJ/mol/rad^2.

Now, to make things even more complicated, radians is natural and
not really a physical unit, so it is quite common to leave them out in 
papers :-)

It looks as if the paper uses the "type 1" angle definitions - you can 
either
translate them (to first order) or just mix type 1 and type 2 angles in 
your topology.


Cheers,

Erik