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Hi<br>
<br>
Well, according to the link you pointed out, the Widom technique
gives you the excess chemical potential, as we discussed. mu and
mu_ideal (in your link) are not calculated, those are just the
reference states between which the Widom technique calculates the
excess chem pot. <br>
<br>
As I said, I think U_{n+1} refers to the interaction energy of the
inserte particle with the system, but maybe someone could confirm or
correct.<br>
<br>
Javier<br>
<br>
El 16/05/12 11:44, Steven Neumann escribió:
<blockquote
cite="mid:CAKZJqQGaeYJ=u70Ps4nfrn7MxamyWQvSrwokf2dVL0Kb+e7asQ@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Wed, May 16, 2012 at 10:28 AM, Javier
Cerezo <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jcb1@um.es" target="_blank">jcb1@um.es</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> About the red curve, I
guess fluctuations might be directly related to volume
fluctuations, you can extract the volume over time from
g_energy (boxXX*boxYY**boxZZ) and compare. (just another
comment, now I am not very sure about the "f." that precedes
the red line legend..)<br>
<br>
About the interpretation of the quantities, the Widom
technique does not provide you with an absolute value of the
chemical potential but directly with the excess chemical
potential. So, mu=-kTlog(Ve ^ (U*B)/(V))n+1 is the excess
chemical potential, where (if I recall correctly) U_{n+1} is
the the interaction energy between the inserted particle
and the rest of the system. You don't need (and should not
do) such post-processing operations that you proposed to get
the excess chemical potential.<br>
<br>
Javier<br>
</div>
</blockquote>
<div><br>
Thank you.<br>
In this case I am considering the curve with NPT - with
volume. <br>
<br>
From the equation u=-kTlog(Ve ^ (U*B)/(V))n+1 (the one on the
plot - if it is correct! Or it should be with delta?) we will
obtain the chemical potential of the system with N+1
molecules. To obtain the excess we need to have chemical
potential of the system wit N particles and the substract it
according to the equation:<a moz-do-not-send="true"
href="http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method">http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method</a><br>
If it is a mistake and there is deltaU this is the exceess, if
not this is only for N+1. Please, correct me if I am wrong.<br>
<br>
Steven<br>
</div>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> <br>
<br>
El 16/05/12 11:06, Steven Neumann escribió:
<div>
<div class="h5">
<blockquote type="cite">Thank you very much! I just saw
your response.<br>
<br>
As I run it in NPT ensemble the plot with volume is
important for me. Please, See the plot:<br>
<br>
<a moz-do-not-send="true"
href="http://speedy.sh/CJn5b/tpiN.jpg"
target="_blank">http://speedy.sh/CJn5b/tpiN.jpg</a><br>
<br>
So does the fluctuating red curve make any sesnse then
if it does not consider volume?<br>
<br>
Another thing: this is chemical potential of the
system with extra water molecule (N+1), right
(u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want to obtain
the excess chemical potential:<br>
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it
for the system with N molecules and then substract it.
<br>
Is it calculated somewhere or I should use g_energy of
my previosu system and calculate the total potential
energy then -kTlog... of this values and then
substract it? Please correct me if I am wrong.<br>
<br>
Steven<br>
<br>
<br>
<div class="gmail_quote">On Tue, May 15, 2012 at 11:59
AM, Javier Cerezo <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:jcb1@um.es"
target="_blank">jcb1@um.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Steven.
<div><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">
<div>1. Why this value is divided by nm3?
Shall I multiply it by the simulation
box?<br>
</div>
</div>
</blockquote>
</div>
It is not not divided by nm3. The legend for "y"
axis is not appropriate for your plot. Keep in
mind that the same graph is used to represent
lots of quantities (you can plot all of them
with xmgrace -nxy tpi.xvg). The "y" axis is not
the same for all, but only one label is
possible, so developers have to chose which
label to place on the axis. But this is just a
label, don't give much importance to it and
analyse you results (including units) according
to the equations and the standard units in
gromacs.
<div><br>
<blockquote type="cite">
<div class="gmail_quote">
<div>2. Why e^(-BU) is multiplied by V? I
just want to have the excess chemical
potential: u=-kTlog(e ^ (-deltaU*B) - so
how can I get deltaU?<br>
</div>
</div>
</blockquote>
</div>
The volume appears in the expression of the
excess chemical potential if you are running a
NpT ensemble. The second plot (if you use
xmgrace -nxy tpi.xvg) does not contain the
volume.
<div><br>
<blockquote type="cite">
<div class="gmail_quote">
<div> 3. The value corresponds to the
plateau so I should run it for longer
time?<br>
</div>
</div>
</blockquote>
</div>
You are getting a time&ensemble average and
for large sampling (and large simulation times),
this average should converge. So, the final
value you will get is the last point of the
graph, it up to you to say if it is converged.
So you can try to enlarge the number of points
sampled, if the shape does not change you are
sampling correctly every snapshot, then take
longer simulation times if you want to converge
your results.<br>
<br>
Javier<br>
<br>
<br>
El 15/05/12 09:57, Steven Neumann escribió:
<div>
<div>
<blockquote type="cite"><br>
<br>
<div class="gmail_quote">On Mon, May 14,
2012 at 5:05 PM, Justin A. Lemkul <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div>
<div><br>
<br>
On 5/14/12 11:53 AM, Steven
Neumann wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> Dear
Gmx Users,<br>
<br>
Did anyone use TPI method for
the calculation of chemical
potential? The tpi.xvg<br>
files consists of:<br>
<br>
@ s0 legend "-kT
log(<Ve\S-\xb\f{}U\N>/<V>)"<br>
@ s1 legend "f. -kT
log<e\S-\xb\f{}U\N>"<br>
@ s2 legend "f.
<e\S-\xb\f{}U\N>"<br>
@ s3 legend "f. V"<br>
@ s4 legend "f.
<Ue\S-\xb\f{}U\N>"<br>
@ s5 legend "f. <U\sVdW
System\Ne\S-\xb\f{}U\N>"<br>
@ s6 legend "f. <U\sdisp
c\Ne\S-\xb\f{}U\N>"<br>
@ s7 legend "f. <U\sCoul
System\Ne\S-\xb\f{}U\N>"<br>
@ s8 legend "f. <U\sCoul
recip\Ne\S-\xb\f{}U\N>"<br>
<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "(kJ
mol\S-1\N) / (nm\S3\N)"<br>
<br>
Can anyone explain me these
legends? I just want obtain a
value of the excess<br>
chemical potential according to
the equation:<br>
u=-kT log (-deltaV/kT), Which
legend is responsible for this
and what are the<br>
units? kJ/mol? Please, explain
as the above letters does not
mean to me anything?<br>
<br>
</blockquote>
<br>
</div>
</div>
These strings are formatted for
XmGrace. Have you tried plotting the
file to see what it contains? The
legends will be far more obvious if
you do.<br>
<br>
-Justin<span><font color="#888888"><br>
</font></span></blockquote>
<div><br>
Thank you Justin. <br>
Can anyone explain me from the plot:<br>
<br>
<a moz-do-not-send="true"
href="http://speedy.sh/Xpnws/tpi.JPG"
target="_blank">http://speedy.sh/Xpnws/tpi.JPG</a><br>
<br>
1. Why this value is divided by nm3?
Shall I multiply it by the simulation
box?<br>
2. Why e^(-BU) is multiplied by V? I
just want to have the excess chemical
potential: u=-kTlog(e ^ (-deltaU*B) -
so how can I get deltaU?<br>
3. The value corresponds to the
plateau so I should run it for longer
time?<br>
<br>
<br>
Thank you,<br>
<br>
Steven<br>
<br>
</div>
<blockquote class="gmail_quote"
style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex"> <span><font
color="#888888"> <br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a
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href="http://vt.edu"
target="_blank">vt.edu</a> | <a
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<span><font color="#888888">
<div>-- <br>
Javier CEREZO BASTIDA<br>
PhD Student<br>
Physical Chemistry<br>
Universidad de Murcia<br>
Murcia (Spain)<br>
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<pre cols="72">--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434</pre>
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<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
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30100, Murcia (SPAIN)
T: (0034)868887434</pre>
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