[gmx-users] Unstable model : need suggesstion

[Sukesh Chandra Gain]

Dear All,
I have done a simulation (in water) of PfPBGD model protein for 500 ps.
But when I compared the secondary structure of my native protein structure
vs structure after simulation. I observed that lot of unfolding is
happening after simulation.
So, my queries are:
1> Is there any way I can improve my model so that model protein become
stable?
2> Is there any problem with my parameters which i have used for energy
minimization, Position restrained dynamics and final simulation?
3> Can I improve my result changing the parameter files?

what are the changes required?

These are the parameters I have used for different run:

em.mdp:
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt		    =  0.002   ;ps
nsteps              =  400
;
;	Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no


pr.mdp:

title               =  Yo
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  10000	; total 20 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype	    =  PME
rcoulomb            =  1.0
rvdw                =  1.4
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  Protein	SOL   CL-
tau_t               =  0.1	0.1   0.1
ref_t               =  300	300   300
; Energy monitoring
energygrps	    =  Protein	SOL   CL-
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


full.mdp:

title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  250000	; total 500 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  Protein	SOL  CL-
tau_t               =  0.1	0.1  0.1
ref_t               =  300	300  300
; Energy monitoring
energygrps          =  Protein  SOL  CL-
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529

I expect suggestion from expert.

Thanks,
Sukesh