<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>It is always better to keep the discussion in the list. Someone </div><div>could benefit of it as well as you from others.</div><br><div><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Lum Nforbi <<a href="mailto:lumngwegia@gmail.com">lumngwegia@gmail.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">January 4, 2010 7:57:04 PM GMT+01:00</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>Thank you for reply on RDF PLOT problem/Question.</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div>Hi Xavier,<br><br>Is there something I can do in order to eliminate this peak, maybe like making adjustments to my coordinate file?<br></blockquote>In your coordinates no, but you can just erase it. I am not actually sure of </div><div>how the normalization of the rdf is done considering that this pick should not </div><div>appear in the analyses! </div><div><br></div><div>Either someone else knows or you have to find out our self, looking at the code </div><div>or in the archive :))</div><div><blockquote type="cite"><br>Thank you,<br> Lum<br><br><br>Message: 3<br> Date: Sun, 3 Jan 2010 13:18:29 +0100<br> From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br> Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot?<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <<a href="mailto:28FDB30B-7B96-4975-BD1D-D6120F1B4BEA@rug.nl">28FDB30B-7B96-4975-BD1D-D6120F1B4BEA@rug.nl</a>><br> Content-Type: text/plain; charset="us-ascii"<br> <br> <br> I am not sure somebody gave you an answer ...<br> <br> the first intense and probably very narrow pick is very<br> likely due to the intramolecular OH distance. It should be<br> around 0.1 nm, isn't it?<br> <br> On Jan 1, 2010, at 3:53 AM, Lum Nforbi wrote:<br> <br> ><br> ><br> > ---------- Forwarded message ----------<br> > From: Lum Nforbi <<a href="mailto:lumngwegia@gmail.com">lumngwegia@gmail.com</a>><br> > Date: Thu, Dec 31, 2009 at 12:33 PM<br> > Subject: What could be wrong with rdf plot?<br> > To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> ><br> ><br> > Dear all,<br> ><br> > I am currently analyzing a system of 2000 molecules of TIP3P<br> > water on which I performed a NPT simulation. The plot for g(OO)<br> > looks very good but for some reason unknown to me, on the g(OH) plot<br> > there is an intense peak coming before the normal peaks that are<br> > characteristic of a g(OH) plot. Could someone tell me what is going<br> > on? I have attached the graphs for gOO and gOH for viewing.<br> > Also, I have still not been able to figure out how to calculate<br> > the Cp of my system and I have been struggling with this for over a<br> > month now. g_energy for my system gives a wrong Cv (~12). Can<br> > someone explain to me or give me hints on how to calculate the Cp of<br> > an NPT simulation of TIP3P water, please?<br> ><br> > Have a wonderful New Year 2010 and Decade (2010-2019)!<br> ><br> > Thank you,<br> > Lum<br> ><br> ><br> > <RDF_OWHW1HW2_0_8000PS>--<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" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br> > posting!<br> > Please don't post (un)subscribe requests to the list. Use the<br> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> <br> -------------- next part --------------<br> An HTML attachment was scrubbed...<br> URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100103/ef8adddd/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100103/ef8adddd/attachment-0001.html</a><br> <br></blockquote></div><br></body></html>