On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo <[email protected]> wrote: > About the red curve, I guess fluctuations might be directly related to > volume fluctuations, you can extract the volume over time from g_energy > (boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not very > sure about the "f." that precedes the red line legend..) > > About the interpretation of the quantities, the Widom technique does not > provide you with an absolute value of the chemical potential but directly > with the excess chemical potential. So, mu=-kTlog(Ve ^ (U*B)/(V))n+1 is the > excess chemical potential, where (if I recall correctly) U_{n+1} is the the > interaction energy between the inserted particle and the rest of the > system. You don't need (and should not do) such post-processing operations > that you proposed to get the excess chemical potential. > > Javier >
Thank you. In this case I am considering the curve with NPT - with volume. >From the equation u=-kTlog(Ve ^ (U*B)/(V))n+1 (the one on the plot - if it is correct! Or it should be with delta?) we will obtain the chemical potential of the system with N+1 molecules. To obtain the excess we need to have chemical potential of the system wit N particles and the substract it according to the equation: http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method If it is a mistake and there is deltaU this is the exceess, if not this is only for N+1. Please, correct me if I am wrong. Steven > > > El 16/05/12 11:06, Steven Neumann escribió: > > 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 <%28540%29%20231-9080> >>> 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 >> > > > > > -- > Javier CEREZO BASTIDA > Ph.D. Student > Physical Chemistry > Universidad de Murcia > 30100, Murcia (SPAIN) > T: (0034)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 >
-- 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
