NEB is very different in various amber versions. Please specify which you
used.
On Sep 16, 2010 12:29 PM, "Abhishek Singh" <asingh7.ncsu.edu> wrote:
Dear All
I am trying to use nudged elastic band method (NEB) to calculate the lowest
energy path between two conformations of a ssDNA 320-atom molecule. I Have a
situation that in the cooling stage the temperature does not goes to zero K.
I tried reproducing the tutorial example and the results match. Shown below
is the input and output files. Please suggest.
Input file for cooling
&cntrl
imin = 0, irest = 1,
ntx=5,
ntc=1,
ntf=1,
ntpr=500,
ntwx=10000,
ntb = 0, cut = 999.0,
rgbmax=999.0,
igb = 1,
saltcon=0.2,
nstlim = 120000, nscm=
0,
dt =
0.001,
ntt = 3,
gamma_ln=1000.0,
temp0...
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 120000 TIME(PS) = 540.000 TEMP(K) = 3.07 PRESS =
0.0
Etot = -29617.569...
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Received on Thu Sep 16 2010 - 10:00:03 PDT
