Hi David,<br>
Thanks for your kindly reply.<br>Because I am simulating a pure fluid system, I used the epsilon-r = 1in the .mdp file. <br>_____________________________________________________<br>
coulombtype = pme<br>
rcoulomb-switch = 0<br>
rcoulomb = 1.1<br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>
epsilon-r = 1<br>
_____________________________________________________<br><br> If I don't use the Reaction-Field method, how should I use the -rpsilonRF option? (I want to use 0. But because 0 means infinity here, I have no idea how to use it) I calculated dielectric constant with and without "-esilonRF" option, please see the following results
<br>
_____________________________________________________<br>g_dipoles -temp 425 -f md2 -s md2 -enx md2.edr<br>Epsilon = 826.496<br><br>g_dipoles -temp 425 -epsilonRF 1 -f md2 -s md2 -enx md2.edr<br>Epsilon = -2.01094<br>
_____________________________________________________<br><br>Neither result are the values what I expect. What wrong?<br><br><br><br><div><span class="gmail_quote">2006/11/13, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@xray.bmc.uu.se</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Qiao Baofu wrote:<br>> Hi all,<br>><br>> I have some question about calculating dielectric constant:<br>> 1. From the manual, it seems that there are two methods to calculate the<br>> dielectric constant: a. use g_dipoles -temp 400 -f -s directly, b) use
<br>> g_dipoles -nonormalize -corr total -c dipcorr.xvg, then g_dielectric -f<br>> dipcorr.xvg -o epsw.xvg. (Please correct me if the commandlines are<br>> wrong). Thus I want to know the difference between them.
<br><br>g_dielectric does another analyis. You want to run g_dipoles either with<br>the -enx flag or with a trajectory.<br><br>> 2. If I want to calculate the dielectric constant, must I use the<br>> Reaction Field in the couloumbtype? Now I have some results from PME.
<br>> Can I use these results directly to calculate the dielectric constant?<br><br>PME is fine. You have to supply the right dielectric constant to the<br>program (though the default of 0 == infinity) is what most people use.
<br></blockquote><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">><br>> Thanks very much in advances!<br>><br>><br>><br>> Sincerely yours,
<br>> Baofu Qiao<br>><br>><br>> <br>--<br>David.<br>________________________________________________________________________<br></blockquote></div><br><br clear="all"><br>