<br /><br /><span>On 01/24/11, <b class="name">Archana Sonawani </b> <ask.archana@gmail.com> wrote:</span><blockquote cite="mid:AANLkTim661aZfYO-u4=q6HpT3FLYk6XX0eC6DcXfrFVQ@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div>Hello,</div>
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<div>I have run 10 ns simulation for ligand-receptor complex. For analysis, I checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist. </div>
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<div>In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , but after 5ns I get long vertical lines upto 2.5 nm. I dont know whats the reason for that. I am sending the RMSD plot as attachment.</div>
<div>These lines are not seen in case of hydrogen bond plot and distance plot. Please help me out.</div>
<div ><br/></div></div></blockquote>These are almost certainly periodicity artefacts. Look at your trajectory in a suitable visualization algorithm, and you will see (parts of) the complex cross boundaries at those points. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for discussion and solution approaches.<br /><br />Mark<br /><blockquote cite="mid:AANLkTim661aZfYO-u4=q6HpT3FLYk6XX0eC6DcXfrFVQ@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div ><br/></div></div></blockquote>