<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span></span></div><div><br></div> <div style="font-family: bookman old style, new york, times, serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> ----- Forwarded Message -----<br> <b><span style="font-weight:bold;">From:</span></b> mohammad agha <mra_bu@yahoo.com><br> <b><span style="font-weight: bold;">To:</span></b> "gmx-users@gromacs.org" <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, January 31, 2012 11:56 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> g_rdf<br> </font> </div> <br>
<div id="yiv404596587"><div><div style="color:#000;background-color:#fff;font-family:bookman old style, new york, times, serif;font-size:14pt;"><div>Dear Prof.</div><div><br></div><div>I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf. Then I count the number of atoms in the shells around the COM of special group by " trjorder -com -nshell -r " , next I use from this formula for compute the density:</div><div>density = (dN/4*pi*dr*r^2)*g(r), where dN, dr, r and g(r) are the number of atoms in each shell, wide of shell, radius of COM of special group, and averaged RDF in each shell, respectively.</div><div>While the plot of g(r) is consistent with published previous results but density has not consistence with them, I think that I am wrong in compute the density.</div><div>Please help me.</div><div><br></div><div>Best
Regards</div><div>Sara<br><i></i></div></div></div></div><br><br> </div> </div> </div></body></html>