[gmx-users] Energy minimization

[Malihe Hasanzadeh]

Hi,
I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I
do energy minimization, my system is converged but has positive potential
energy. also this step only takes 3 second! for next step (pr), gives error:
your system is not equilibrated well and blowing up! I chcked my em.pdb
file and
I saw the Sol box is separated from protein and DNA!
Could you please help me, what should I do?what part of my set is wrong?

my em.mdp:
define = -DFLEXIBLE
integrator = cg ; steep
nsteps = 4000
nstlist = 1
constraints = none
emtol = 100.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
nstcalcenergy = 1.2
ewald_rtol = 1e-05
coulombtype = PME
cutoff-scheme = Group
ns_type = grid
rlist = 1.4
rcoulomb =1.4
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes

Sincerely,
Malihe