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..)
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.
Javier
El 16/05/12 11:06, Steven Neumann escribió:
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does not
consider volume?
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:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system
with N molecules and then substract it.
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.
Steven
On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo <[email protected]
<mailto:[email protected]>> wrote:
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
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.
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?
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.
3. The value corresponds to the plateau so I should run it for
longer time?
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.
Javier
El 15/05/12 09:57, Steven Neumann escribió:
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>> wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical
potential? The tpi.xvg
files consists of:
@ s0 legend "-kT log(<Ve\S-\xb\f{}U\N>/<V>)"
@ s1 legend "f. -kT log<e\S-\xb\f{}U\N>"
@ s2 legend "f. <e\S-\xb\f{}U\N>"
@ s3 legend "f. V"
@ s4 legend "f. <Ue\S-\xb\f{}U\N>"
@ s5 legend "f. <U\sVdW System\Ne\S-\xb\f{}U\N>"
@ s6 legend "f. <U\sdisp c\Ne\S-\xb\f{}U\N>"
@ s7 legend "f. <U\sCoul System\Ne\S-\xb\f{}U\N>"
@ s8 legend "f. <U\sCoul recip\Ne\S-\xb\f{}U\N>"
@ xaxis label "Time (ps)"
@ yaxis label "(kJ mol\S-1\N) / (nm\S3\N)"
Can anyone explain me these legends? I just want obtain a
value of the excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for
this and what are the
units? kJ/mol? Please, explain as the above letters does
not mean to me anything?
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.
-Justin
Thank you Justin.
Can anyone explain me from the plot:
http://speedy.sh/Xpnws/tpi.JPG
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
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?
3. The value corresponds to the plateau so I should run it for
longer time?
Thank you,
Steven
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434 <tel:%28%2B34%29868887434>
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
