[gmx-users] protein domain separate

[hazizian]

Hi
As I told in my perevious mail, My system consist of a 2-domain protein 
(Domain A and B), even when I did EM minimization this 2 damain separated.

my em.mpf is: 

title               =  n.pdb
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
nsteps              =  40000
constraint_algorithm  = shake
shake_tol           = 0.0001
nstenergy           =  10
nstxtcout           =  10
nstlist             =  5
ns_type             =  grid
rlist               =  1.2
coulombtype         =  PME
rcoulomb            =  1.2
rvdw                =  1.4
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes

;       Energy minimizing stuff
;
emtol               =  10.0
emstep              =  0.01

Also it is not because of pbc, 
What do you suggest for solving this, thank you very much for replying.  
--
Tehran University of Medical Sciences
www.tums.ac.ir


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