[gmx-users] Ion distribution around Cl fix

[Mark Abraham]

On 7/07/2011 6:25 PM, Javier Cerezo wrote:
> 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?

Indeed. Also, knowing what is in your index groups and the commands that 
produced the graphs is integral to attempting to interpret the results, 
and we're still in the dark.

When you go to a doctor and say "I've got these two lumps, and they're 
different and I'm not sure I should have either of them, or that they 
should look this way", then you're paying the doctor lots of money to 
ask questions about where the lumps are and how long they've been there 
and whether you got bitten by insects and to actually look at the lumps 
and to pat you on the head and say they'll probably be gone by the 
weekend and to maybe invest in some mosquito screens and not scratch 
open one of them. :-)

But when you're hoping someone will give up their time for free to help 
solve your problem... do give as much information as you think could 
possibly be relevant on your first attempt :-)

Mark

>
> 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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