<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR><DIV><DIV>On Oct 10, 2005, at 5:10 PM, Rama Gullapalli wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear GMX ers</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I had a simple question regarding the calculation of</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">lipid diffusion.<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1) How do i remove the supradiffusivity of the bilayer</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">when calculating the diffusion constant?</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If you haven't started the simulation yet, define three separate groups for center-of-mass motion removal: water and a separate group for each lipid layer.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If you already started it, you can use a trick that might require some coding. Go through the trajectory, remove periodicity and calculate the center-off-mass for each frame. Calculate how much the COM moves, and then remove this motion from each frame.</DIV><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2) How do i couple the COM removal of the individual</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">bilayer leaflets while running the simulation? Is it</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">through make_ndx, assign names and couple them</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">seperately? Also, is it necessary to do the same in</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">order to obtain correct diffusion coefficients?</DIV></BLOCKQUOTE></DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">You've essentially got it :-)</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">The COM motion needs to be taken into account one way or the other, since the periodic system means there isn't any natural friction for collective XY motion. Doing it before is easier, but we managed to publish the first reasonably accurate diffusion constants by coming up with the second method - 100ns of trajectories was a lot at the time, and we weren't exactly thrilled with the idea of rerunning it all :-)</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">Cheers,</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD">Erik</FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV></BODY></HTML>