[gmx-users] Ion distribution around Cl fix

[Javier Cerezo]

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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