Many thanks. Then what is the range of dihedral angle (-180 to 180 or 0 to
360) it would dump to the file ? Is there someway I can restrict output
angles to be written between -180 to 180 or 0 to 360 ?
Thanks,
Mishra
On Thu, May 12, 2016 at 11:05 PM, David Cerutti <dscerutti.gmail.com> wrote:
> In my experience it does not matter; you can even specify angles beyond 360
> and it will re-image them as needed.
>
> On Thu, May 12, 2016 at 9:58 AM, mish <smncbr.gmail.com> wrote:
>
> > Dear all,
> >
> > I am running umbrella sampling simulations using pmemd (cuda) from
> > Amber14. In these calculations I want to construct PMF for rotating a
> > dihedral angle of an molecule by 360 degree. I am am slightly confused
> over
> > the range of input dihedral angle in input "DISANG" file. Should it be
> from
> > -180 to 180 or from 0 to 360. One of the calculations went with 0 to 360
> > but in another one I am getting negative values (between 10 and -10)
> dumped
> > for window at 0 degree. Should I simply convert them between 0 and 360
> and
> > construct PMF ? Example file disang.270 is as follows :
> >
> > -------------
> >
> > harmonic restraints for 270 deg
> >
> > &rst
> >
> > iat=2913,2915,2918,2932,
> >
> > r1=210.0, r2=270.0, r3=270.0, r4=330.0,
> >
> > rk2=200, rk3=200,
> >
> > &end
> >
> >
> > Best,
> >
> > Mish
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> > AMBER.ambermd.org
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> >
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Received on Thu May 12 2016 - 16:30:03 PDT
