[gmx-users] Is something wrong wih my mdp?

[chenxianli]

Hi all! 
  Recently I have been doing the MD simulation about the ratio of opening
and closing of RNA base pais in different Na ion concentrations. Runing 20
ns simulation using  Gromacs. 

As far as I know,in most articles on this problem saying: the higher Na ion
concentration ,the more stable of RNA structure,so the probility of base
pair opening will decrease .But I can't get the same results...  Does anyone
konw why ? 
After runing equilibrium, my mdp file is as follows: 



title                   = 1ZIH 
define                   = -DPOSRES 
cpp                     = /lib/cpp 
constraints             = all-bonds 
;run parameters 
integrator          =  md 
dt                  =  0.002	                   ; ps 
nsteps              =  1000000	               ; total 0.2ns 
nstcomm             =  100 
;output control 
nstxout             =  1000                     ; collect data every 2 ps 
nstxtcout           =  1000 
nstvout             =  1000 
nstfout             =  0 
nstlog              =  1000 
nstcalcenergy       =  100                     ;frequency fo calculating the
energy 
nstenergy           =  1000                    ;frequency to write energies
to energy file 
;Bond parameter 
continuation           = no                     ;no constant restarting 
constraint-algorithm   = lincs 
lincs_iter             = 1 
lincs_order            = 4 
;Neighborsearching 
ns_type                =  grid 
nstlist                =  5 
rlist                  =  1.0 
rcoulomb               =  1.0 
vdwtype                =  cut-off 
rvdw                   =  1.0 
;Electrostatics 
coulombtype          =  PME 
pme_order	      =  4 
fourierspacing	      =  0.12             

;Temperature coupling is on 
Tcoupl              = V-rescale                     ;berendsen 
tc-grps             = RNA      SOL    NA   CL   
Tau_t               = 0.1      0.1   0.1   0.1 
ref_t               = 350      350   350   350   

; Berendsen  Pressure coupling is on 
Pcoupl                  = Parrinello-Rahman 
refcoord-scaling        = all 
Pcoupltype              = isotropic 
tau_p                   = 0.5 
compressibility         = 4.5e-05 
ref_p                   = 1.0 

;Periodic boundary conditions 
pbc                     = xyz 

;Dispersion correction 
DispCorr                = EnerPres 

; Generate velocites is on at 300 450 500 550 K. 
gen_vel                 = yes 
gen_temp                = 350 
gen_seed                = 173529 


Is something wrong with my mdp file? 
Thanks ！

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