[gmx-users] Abnormal popc struture after inserting protein

[minnale]

Hi all, 
     I have embedded protein into POPC bilayer, I accomplished energy minimisation 

em.mdp file

cpp                 = /usr/bin/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
nsteps              =  500

;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.01
nstcomm             =  1.0
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.4
Tcoupl              =  no
Pcoupl              =  no

its showed following sentences

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 104 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -2.2754422e+05
Maximum force     =  2.3355256e+03 on atom 913
Norm of force     =  9.4749170e+03

gcq#191: "These Gromacs Guys Really Rock" (P.J. Meulenhoff)

  So I dont boughter about those sentences because I confirmed in list archives that I can proceed further steps and moreover em.gro file is       fine, so I went for restrain, here I am getting abnormal POPC structure 
means POPC tails are tilting, water molecules structure also disturbed.

Could you please tell me where iam doing mistake?

my pr.mdp filetitle               =   protein in popc restrained
define              =  -DPOSRES_protein
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  10000    ; total 50 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.4
pbc                 =  xyz
; Berendsen temperature coupling is on in three groups
Tcoupl              =  Berendsen
tc-grps             =  POPC    Protein   SOL_CL-
tau_t               =  0.1      0.1       0.1
ref_t               =  310      310       310
; Anisotropic pressure coupling is now on
Pcoupl              =  berendsen
pcoupltype          =  anisotropic
tau_p               =  1.0      1.0     1.0     0        0       0
compressibility     =  4.5e-5   4.5e-5  4.5e-5  0        0       0
ref_p               =  1.0      1.0     1.0     0        0       0
; Energy monitoring
energygrps          =  POPC   Protein   SOL_CL-
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  310.0
gen_seed            =  173529

Thanks in advance.                        
 
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