# [gmx-users] Test Particle Insertion

Steven Neumann s.neumann08 at gmail.com
Wed May 16 11:06:49 CEST 2012

```Thank you very much! I just saw your response.

As I run it in NPT ensemble the plot with volume is important for me.

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 <jcb1 at 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 <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
>>
>> ========================================
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>
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Murcia (Spain)
> Tel: (+34)868887434
>
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