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
<<attachment: RDF Cl around Cl fix.png>>
<<attachment: RDF Na around Cl fix.png>>
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