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Hi,<br><br>Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot is set from the initial frame.<br>So if your volume fluctuates a lot, you might have incorrect normalization very close to the cut-off.<br>But in "normal" liquid simulations the box length will never change more than 1%.<br><br>Berk<br><br>> Date: Tue, 24 Nov 2009 17:12:44 +0100<br>> Subject: Re: [gmx-users] Normalization in g_rdf<br>> From: ondrej.marsalek@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Hi again,<br>> <br>> I thought pressure coupling is handled by g_rdf. Looking at the code,<br>> it seems that the block starting with:<br>> <br>> /* Must init pbc every step because of pressure coupling */<br>> <br>> takes care of that, so even with a relatively big volume change at the<br>> beginning, it should not be a problem. Is that not the case?<br>> <br>> Ondrej<br>> <br>> <br>> On Tue, Nov 24, 2009 at 16:12, Berk Hess <gmx3@hotmail.com> wrote:<br>> > Hi,<br>> ><br>> > g_rdf limits the distance to half the minimum periodic image distance.<br>> > So the volume normalization is always simply 4 pi r^2.<br>> > It uses the starting unit-cell with a factor of 0.99.<br>> > So you would only see strange effects when the box length reduces<br>> > more than 1% due to pressure coupling.<br>> ><br>> > Berk<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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