[gmx-users] Ion distribution around Cl fix

[Saeid Akbarshahi]

Dear All

I want to simulate a  boxfilledwater that includes 10 sodium ion and 9 chloride ion .
a chlorine fixed placein center of box simulation to see how it affects the distribution ions .
Two graphs were obtained for the distribution of ions than to Cl fix (chlorine fixin center of box)
Question :Do not very highPeak chart  in rdf sodiumthan to Cl fix?

The total electrical charge = 10 + (-10) = 0

Box : 2.65 *2.65 *2.65 nm
force field : AMBER99SB-ILDN

Number of Na : 10 

Number of Cl : 9
Number of Cl fix  : 1
Time simulation : 4 ns
Water : TIP3P
file.mdp
; Run parameters
integrator    = md-vv        
nsteps        = 2000000       
dt        = 0.002        ; 2 fs
constraints     =  none       
ns_type        = grid       
nstlist        = 5        
rlist        =
 1.0        
rcoulomb    = 1.0        
rvdw        = 1.0       
; Electrostatics
coulombtype    = PME        
pme_order    = 4        
fourierspacing    = 0.15        
ewald_rtol      = 1e-05
optimize_fft    = yes
; Temperature coupling is on
tcoupl        = nose-hoover    
tc-grps        = System    
tau_t        = 0.5       
ref_t        = 298        
pbc        = xyz   
     
DispCorr        = EnerPres
vdw-type        = Cut-off
freezegrps               = Cl fix
freezedim                = Y Y Y


Kind Regard
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