[gmx-users] minimisation converted into machine precision
sharmanitu35 at gmail.com
Sat Apr 25 12:50:26 CEST 2009
After concatanation of protein with lipid I did inflatgro processing
forscaling but I am facinng problem during energy minimisation step of
inflatgro procedure . The minimisation terminated after few step and it
converted into machine precision-
Steepest Descents converged to machine precision in 349 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 4.2808670e+06
Maximum force = 4.9091840e+04 on atom 7290
Norm of force = 8.9087488e+02
As I searched its becoz of clashes between lipid and protein .
Do anyone have idea about how can we avoid these clashes ?whats the
parameter required to avoid this?
the parameter file i am using is like this-
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 10000
; Energy minimizing stuff
emtol = 1000
emstep = 0.001
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
coulombtype = PME
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
comm-mode = Linear
pbc = XYZ
SO please anyone suggest where I am doing fault ?
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