Thank you very much! I just saw your response. As I run it in NPT ensemble the plot with volume is important for me. Please, See the plot:
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 <[email protected]> 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 <[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 | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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