[gmx-users] Test Particle Insertion

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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