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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