<br><br><div class="gmail_quote">On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 5/14/12 11:53 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
<br>
Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg<br>
files consists of:<br>
<br>
@ s0 legend "-kT log(<Ve\S-\xb\f{}U\N>/<V>)"<br>
@ s1 legend "f. -kT log<e\S-\xb\f{}U\N>"<br>
@ s2 legend "f. <e\S-\xb\f{}U\N>"<br>
@ s3 legend "f. V"<br>
@ s4 legend "f. <Ue\S-\xb\f{}U\N>"<br>
@ s5 legend "f. <U\sVdW System\Ne\S-\xb\f{}U\N>"<br>
@ s6 legend "f. <U\sdisp c\Ne\S-\xb\f{}U\N>"<br>
@ s7 legend "f. <U\sCoul System\Ne\S-\xb\f{}U\N>"<br>
@ s8 legend "f. <U\sCoul recip\Ne\S-\xb\f{}U\N>"<br>
<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "(kJ mol\S-1\N) / (nm\S3\N)"<br>
<br>
Can anyone explain me these legends? I just want obtain a value of the excess<br>
chemical potential according to the equation:<br>
u=-kT log (-deltaV/kT), Which legend is responsible for this and what are the<br>
units? kJ/mol? Please, explain as the above letters does not mean to me anything?<br>
<br>
</blockquote>
<br></div></div>
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.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br></font></span></blockquote><div><br>Thank you Justin. <br>Can anyone explain me from the plot:<br><br><a href="http://speedy.sh/Xpnws/tpi.JPG">http://speedy.sh/Xpnws/tpi.JPG</a><br>
<br>1. Why this value is divided by nm3? Shall I multiply it by the simulation box?<br>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?<br>
3. The value corresponds to the plateau so I should run it for longer time?<br><br><br>Thank you,<br><br>Steven<br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<span class="HOEnZb"><font color="#888888">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br>