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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 12 2016 - 07:00:03 PDT
