<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>You may have wanted to have sent the message to the gmx list!<div><br></div><div>XAvier.<br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><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">nicoletta liguori <<a href="mailto:fisicotta@gmail.com">fisicotta@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">July 26, 2011 5:28:29 PM MDT (CA)</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"><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>density error bars</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div>Hi,<div>I'm using Gromacs and its tools to sample some kind of membranes and characterize their features.</div><div>Actually I don't know what to do about error bars.</div><div>For example when I calculate the density mass distribution along the axis parallel to the normal to the </div> <div>membrane surface I average on all trajectories using g_density_d on my set contained</div><div>in the .xtc file.</div><div>Considering that, for what I understood, it makes the average on time of the density, but without</div> <div>adding any kind of error (there are no possibilities with this tool) I tried to check if there are other tools</div><div>available to calculate the error bars but seem not to exist!!</div><div>For example g_analyze reads directly the already averaged set of data (in this case) cause the only</div> <div>possible input is a .xvg file!</div><div>So I was thinking to (not yet know how, is my first computational trial) to calculate the error with a simple</div><div>standard deviation (I was thinking to use matlab ), but to do this, I suppose that</div> <div>I have to consider all the points indipendent, and to do this</div><div>I'd have to look at the autocorrelation function of density itself!</div><div>but how to do this??</div><div>there are again no tools available</div> <div>how do you do when u deal with errors?</div><div>Thanks for attention and for the help</div><div>Nicoletta</div></blockquote></div><br></div></body></html>