Thanks jason for the clarification. I just referred gamma as phase lag (or
phase shift), a general terminology used when stating a cosine or sine
function.
Arun
Srikanth
On Wed, Oct 8, 2014 at 10:19 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, 2014-10-08 at 10:09 -0400, Arun Srikanth wrote:
> > Hello Amber users.
> >
> > I am using LAMMPS for my simulation with GAFF forcefield. I would like to
> > assign dihedral types correctly in my simulation.
> >
> > I used parmchk2 with -a option to get all the parameters for my
> molecule. I
> > would like to know what the numbers signify with respect to the dihedral
> > expression in GAFF vn, n, phi, gamma. The following is from parmchk-2
> >
> > c3-c3-n3-c3 1 0.300 0.000 -3.000
> > c3-c3-n3-c3 1 0.480 180.000 2.000
> > c3-c3-n3-hn 1 0.300 0.000 3.000
> > c3-n3-c3-h1 1 0.300 0.000 3.000
> > c3-c3-c3-c3 1 0.180 0.000 -3.000
> > c3-c3-c3-c3 1 0.250 180.000 -2.000
> >
> > It would extremely helpful to know which column signifies vn, n and gamma
> >
> > I am not sure about this
> >
> > First col=n
> > second =Vn
> > third=phi
> > fourth is gamma ??(the phase lag)
>
> I'm not sure what you mean by "phase lag". The fourth column is the
> periodicity. A negative sign means that the torsion parameter includes
> the next term.
>
> You can find more information on Amber file formats from
> http://ambermd.org/formats.html
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Oct 08 2014 - 08:00:02 PDT
