[gmx-users] Test Particle Insertion

[Javier Cerezo]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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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>
>

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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