[gmx-users] angle parameters in G96
Erik Lindahl
lindahl at stanford.edu
Fri Jan 31 21:46:52 CET 2003
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
More information about the gromacs.org_gmx-users
mailing list