Hi
The large peak in sodium rdf should be a consequence of the attractive
interaction between Na+ and Cl- and so it seems a reasonable plot.
Please, try to be a bit more clear and specific about your actual
problem. You can also post your command line arguments for rdf.
Also, in your mdp parameters you've set
freezegrps = Cl fix
This means you have 2 different groups ("Cl" and "fix"), is this one
your working mdp file?
Javier
El 07/07/11 09:49, Saeid Akbarshahi escribió:
Dear All
I want to simulate a boxfilledwaterthat includes 10 sodium ionand 9
chloride ion .
a chlorine fixed placein center of box simulationto 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
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434
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