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 <j...@um.es
<mailto:j...@um.es>> 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
<jalem...@vt.edu <mailto:jalem...@vt.edu>> 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
========================================
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