<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Hi,</div><div> 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> 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><br></div><div>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><br></div><div><br></div><div><br></div><div>Thanks</div><div>Jagannath</div><div style="position:fixed"></div>
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