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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Received on Thu May 12 2016 - 07:30:03 PDT
