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On 7/07/2011 6:25 PM, Javier Cerezo wrote:
<blockquote cite="mid:4E156D6C.9050406@um.es" type="cite">
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Hi<br>
<br>
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.<br>
<br>
Also, in your mdp parameters you've set<br>
<span id="yiv230548856result_box" class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">freezegrps = Cl fix<br>
<br>
This means you have 2 different groups ("Cl" and "fix"), is
this one your working mdp file?<br>
</span></span></blockquote>
<br>
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.<br>
<br>
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. :-)<br>
<br>
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 :-)<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4E156D6C.9050406@um.es" type="cite"><span
id="yiv230548856result_box" class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"> <br>
Javier<br>
<br>
<br>
</span></span><br>
El 07/07/11 09:49, Saeid Akbarshahi escribió:
<blockquote
cite="mid:1310024954.71011.YahooMailNeo@web65307.mail.ac2.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 14pt;">
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font-size: 14pt;">
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">
<div id="yiv230548856">
<div style="color: rgb(0, 0, 0); background-color:
rgb(255, 255, 255); font-family: times new roman,new
york,times,serif; font-size: 14pt;">
<div><span></span>Dear All<br>
</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 14pt;">
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">
<div id="yiv230548856">
<div style="color: rgb(0, 0, 0);
background-color: rgb(255, 255, 255);
font-family: times new roman,new
york,times,serif; font-size: 14pt;">
<div> <span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">I</span> <span
title="Click for alternate translations"
class="yiv230548856hps">want</span> <span
title="Click for alternate translations"
class="yiv230548856hps">to</span> <span
title="Click for alternate translations"
class="yiv230548856hps">simulate</span>
<span title="Click for alternate
translations" class="yiv230548856hps">a</span> </span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"></span> <span
title="Click for alternate translations"
class="yiv230548856hps">box</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"> </span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">filled</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"> <span
title="Click for alternate translations"
class="yiv230548856hps">water</span><span
title="Click for alternate translations"
class="yiv230548856hps"></span> <span
title="Click for alternate translations"
class="yiv230548856hps">that</span> <span
title="Click for alternate translations"
class="yiv230548856hps">includes 10 </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">sodium ion</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"></span> <span
title="Click for alternate translations"
class="yiv230548856hps">and 9</span> <span
title="Click for alternate translations"
class="yiv230548856hps">chloride</span>
<span title="Click for alternate
translations" class="yiv230548856hps">ion</span>
<span title="Click for alternate
translations" class="yiv230548856hps"></span>.<br>
<span title="Click for alternate
translations" class="yiv230548856hps"></span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps">a chlorine </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">fixed</span> <span
title="Click for alternate translations"
class="yiv230548856hps">place</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"> <span
title="Click for alternate translations"
class="yiv230548856hps">in center of </span><span
title="Click for alternate translations"
class="yiv230548856hps">box</span></span>
simulation<span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span> <span
title="Click for alternate translations"
class="yiv230548856hps">to</span> <span
title="Click for alternate translations"
class="yiv230548856hps">see</span> <span
title="Click for alternate translations"
class="yiv230548856hps">how it</span> <span
title="Click for alternate translations"
class="yiv230548856hps">affects</span> <span
title="Click for alternate translations"
class="yiv230548856hps">the</span> <span
title="Click for alternate translations"
class="yiv230548856hps">distribution</span>
ions .<br>
<span title="Click for alternate
translations" class="yiv230548856hps">Two</span>
<span title="Click for alternate
translations" class="yiv230548856hps">graphs</span>
<span title="Click for alternate
translations" class="yiv230548856hps">were
obtained</span> <span title="Click for
alternate translations"
class="yiv230548856hps">for the</span> <span
title="Click for alternate translations"
class="yiv230548856hps">distribution</span>
<span title="Click for alternate
translations" class="yiv230548856hps">of
ions</span> than to Cl fix (</span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">chlorine </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">fix</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"> </span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"> <span
title="Click for alternate translations"
class="yiv230548856hps">in center of </span><span
title="Click for alternate translations"
class="yiv230548856hps">box</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en">)<br>
<span title="Click for alternate
translations" class="yiv230548856hps">Question</span>
:<span title="Click for alternate
translations" class="yiv230548856hps"> </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">Do</span> <span
title="Click for alternate translations"
class="yiv230548856hps">not </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">very high</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"> </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">Peak</span> <span
title="Click for alternate translations"
class="yiv230548856hps">chart</span> <span
title="Click for alternate translations"
class="yiv230548856hps"></span><span
title="Click for alternate translations"
class="yiv230548856hps"></span> <span
title="Click for alternate translations"
class="yiv230548856hps">in rdf sodium</span><span
class="yiv230548856" title="Click for
alternate translations"> than to Cl fix?</span></span><span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps"><br>
</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate translations"
class="yiv230548856hps">The total</span>
<span title="Click for alternate
translations" class="yiv230548856hps">electrical
charge = 10 + (-10) = 0<br>
</span></span></div>
<div id="yiv230548856">
<div style="color: rgb(0, 0, 0);
background-color: rgb(255, 255, 255);
font-family: times new roman,new
york,times,serif; font-size: 14pt;">
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Box : 2.65 *</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">2.65 *</span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">2.65 nm<br>
force field : AMBER99SB-ILDN<br>
</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Number of Na
: 10 <br>
</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Number of </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Cl : 9</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Number of </span></span><span
id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Cl fix : 1</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Time
simulation : 4 ns</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Water :
TIP3P<br>
file.mdp<br>
; Run parameters<br>
integrator = md-vv <br>
nsteps = 2000000 <br>
dt = 0.002 ; 2 fs<br>
constraints = none <br>
ns_type = grid <br>
nstlist = 5 <br>
rlist = 1.0 <br>
rcoulomb = 1.0 <br>
rvdw = 1.0 <br>
; Electrostatics<br>
coulombtype = PME <br>
pme_order = 4 <br>
fourierspacing = 0.15 <br>
ewald_rtol = 1e-05<br>
optimize_fft = yes<br>
; Temperature coupling is on<br>
tcoupl = nose-hoover <br>
tc-grps = System <br>
tau_t = 0.5 <br>
ref_t = 298 <br>
pbc = xyz <br>
DispCorr = EnerPres<br>
vdw-type = Cut-off<br>
freezegrps = Cl fix<br>
freezedim = Y Y Y<br>
<br>
</span></span></div>
<div><span id="yiv230548856result_box"
class="yiv230548856" lang="en"><span
title="Click for alternate
translations"
class="yiv230548856hps">Kind Regard<br>
</span></span></div>
</div>
</div>
</div>
</div>
<br>
<br>
</div>
</div>
</div>
</div>
<br>
<br>
</div>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434</pre>
</blockquote>
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