<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Apr 15, 2010, at 3:05 AM, Sanku M wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> I was interested in calculating the diffusion constant of the center of mass of entire lipid-bilayer ( not individual lipid molecules). Regarding this, I had two doubts I wanted to clarify:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> 1. Since I am interested in calculating the diffusion constant of the bilayer iteself, I guess I should allow the drift of the bilayer and hence not then remove the center of mass motion of bilayer (and solvent ) separately. Is that right ? If so, is it still OK to remove the center of mass of whole system ( bilayer + water together ) ? </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2. How to calculate the mean square displacement of center of mass of the entire bilayer. I guess, g_msd program by default, calculate the diffusion constant of the individual atoms or molecules. But, is there a way to get the diffusion constant of the entire bilayer center of mass ? If I specify the index group which consist of all the atoms of the bilayer, will g_msd provide the diffusion constant of its center of mass or it will give the diffusion constant of individual atoms ? I guess, in that case, one should not use -rmcomm option . Is that right ?</div></div></div></span></blockquote>You are right. use g_rms with the lipid bilayer as a group. And removing the COM motion </div><div>during the simulation is what you want to do.</div><div><br></div><div>The question to answer is: is that meaningful? You probably know what you re doing.</div><div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Jagannath</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; position: fixed; "></div></div><br>--<span class="Apple-converted-space"> </span><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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. 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