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
========================================
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Universidad de Murcia
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