[gmx-users] minimisation converted into machine precision

nitu sharma sharmanitu35 at gmail.com
Sat Apr 25 12:50:26 CEST 2009

Dear all

        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 ?

Nitu sharma
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