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I think I coded this all correctly, but the last time I used it was years ago.<br><br>In 3D you could plot G(x), G1(y) and G(z), which are equal for an isotropic liquid.<br>-or plots g(r) which is 2 pi r^2 G(r)<br><br>Berk<br><br><hr id="stopSpelling">From: cari@purdue.edu<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] g_vanhove output<br>Date: Tue, 4 Aug 2009 11:02:51 -0400<br><br>Thanks Berk.<div>I did look at the code, but it is not that easy to understand.</div><div>My conclusion comes from this:</div><div>for a diffusive regime, G(r) should be a gaussian function, with the diffusion</div><div>coefficient characterizing the width.</div><div>I did some tests, and I could match both curves (one from g_vanhove and </div><div>the other from the diff.coef) only if I multiply the output of g_vanhove by r and normalizing again, which makes little sense to me.</div><div>It would be ok to output G(r) or r^2*G(r), but to output r*G(r) seems a mistake</div><div><br></div><div>Thanks again,</div><div>Marcelo</div><div><br></div><div>PS: I did consider the spherical integration.</div><div><br></div><div><br><div><div>On Aug 4, 2009, at 10:41 AM, Berk Hess wrote:</div><br class="EC_Apple-interchange-newline"><blockquote><span class="EC_Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div class="EC_hmmessage" style="font-size: 10pt; font-family: Verdana;">Hi,<br><br>You can look at the code yourself :)<br><br>I coded this and -or (which I assume you are talking about)<br>is G with 1/nm as a unit.<br>It gives the probability that a particle has moved a distance r.<br>The 1/nm is the normalization to make the values bin-size independent.<br><br>Might it be that the difference in interpretation comes from if you consider<br>normalization of the volume of sphere-shells or not?<br><br>Berk<br><br>> From:<span class="EC_Apple-converted-space"> </span><a href="mailto:cari@purdue.edu">cari@purdue.edu</a><br>> To:<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> Date: Tue, 4 Aug 2009 10:25:33 -0400<br>> Subject: [gmx-users] g_vanhove output<br>><span class="EC_Apple-converted-space"> </span><br>> Hi all,<br>> I believe there is a mistake in g_vanhove in version 4.0.5<br>> The 'xvg' output file labels the y axis as G, with nm^-1 as units.<br>> From the units, I guessed that the output was actually r^2 G, however<br>> the initial slope is linear and not quadratic. After a few tries I<span class="EC_Apple-converted-space"> </span><br>> concluded that<br>> the output is actually r*G, which is not something really useful.<br>> I wonder if someone could look at the code and confirm this doubt in<br>> one way or another.<br>><span class="EC_Apple-converted-space"> </span><br>> Many thank,<br>><span class="EC_Apple-converted-space"> </span><br>> Marcelo Carignano.<br>><span class="EC_Apple-converted-space"> </span><br>> PS: I couldn't find this on the list, but it has been difficult to<span class="EC_Apple-converted-space"> </span><br>> access the<br>> archives lately.<br>> _______________________________________________<br>> gmx-users mailing list<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>><span class="EC_Apple-converted-space"> </span><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="EC_Apple-converted-space"> </span>before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<span class="EC_Apple-converted-space"> </span><br>> www interface or send it to<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><hr>See all the ways you can stay connected<span class="EC_Apple-converted-space"> </span><a href="http://www.microsoft.com/windows/windowslive/default.aspx">to friends and family</a><span class="EC_Apple-converted-space"> </span>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="EC_Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="EC_Apple-converted-space"> </span><br>www interface or send it to<span class="EC_Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="EC_Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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