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<DIV><FONT face=Arial size=2>I think that Qiao is right, and I also think that
it's an easy thing to test on a simple test system consisting of a just a
single solute molecule (a single atom to keep it simple) and just a few
solvent molecules (a single one is even easier).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>/Erik Marklund</FONT></DIV>
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style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=qiaobf@gmail.com href="mailto:qiaobf@gmail.com">Qiao Baofu</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, November 22, 2006 1:39
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] radial
distribution function</DIV>
<DIV><BR></DIV>To my knowledge, g_rdf calculate all the atoms of group A to
all the atoms of group B to get the <FONT size=1><FONT
size=4>g</FONT>AB</FONT>(r). g_rdf -com calculate the center of group A, not
the centers of the residues in group A to all the atoms of group B.
<BR><BR>I upload a file based on gmx_rdf.c to calculate the centers of
residues of group A (and B) last month to the website of gromacs. <BR><BR>
<DIV><SPAN class=gmail_quote>2006/11/22, Nguyen Hoang Phuong <<A
href="mailto:phuong@theochem.uni-frankfurt.de">
phuong@theochem.uni-frankfurt.de</A>>:</SPAN>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><BR>My
question is that how does gromacs compute <BR>g(r)? Is r the distance
between center of mass<BR>of the group [ Pep ] and the center of mass of
each<BR>solvent molecule? Or gromacs computes g_i(r) between<BR>each atom of
the group [ Pep] with respect to solvent<BR>molecules and then take average
over all g_i(r) to get<BR>g(r)?<BR><BR>Many thanks in
advance,<BR><BR>Phuong<BR>_______________________________________________<BR>gmx-users
mailing list <A href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</A><BR><A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please
don't post (un)subscribe requests to the list. Use the<BR>www interface or
send it to <A
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't
post? Read <A
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR></BLOCKQUOTE></DIV><BR>Baofu
Qiao<BR>
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