[gmx-users] Test Particle Insertion

[Steven Neumann]

On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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