subarna thakur wrote:
I am doing the energy minimization of a protein using the following
keywords in em.mdp file-
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 3000
;
; Energy minimizing stuff
;
emtol = 1000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
-----------------------------------------------------------------
I am getting the ouput as following---------
Steepest Descents converged to machine precision in 67 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -4.0967048e+06
Maximum force = 3.7720719e+04 on atom 5530
Norm of force = 1.7014005e+02
-----------------------------
Can anybody suggest what changes I can make
Well you can play with the EM step size, or see if atom 5530 looks
unhappy, or you can move on to your equilibration and hope nothing's
seriously wrong.
Mark
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