[AMBER] About harmonic restraints on dihedral angle in pmemd.cuda

From: mish <smncbr.gmail.com>
Date: Thu, 12 May 2016 22:58:21 +0900

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



  r1=210.0, r2=270.0, r3=270.0, r4=330.0,

  rk2=200, rk3=200,



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Received on Thu May 12 2016 - 07:00:03 PDT
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