Dear Dr. van der Spoel:<br>
<br>
Thanks for the clarification in your reply. One more thing I was just curious is that, for C(t) = < f(x).f(x+t) >, <br>
what is the default value for t, which is often called "correlation
time", in gromacs for correlation function calculation, especially in
"g_hbond", <br>
and/or is it possible to customize the t in gromacs? <br><br>best<br>Rama<br><br><div class="gmail_quote">On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">On 2010-02-27 03.27, Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi gromacs users:<br>
As you know autocorrelation function C(t)<br>
<br>
C(t) = <f(0).f(t)><br>
<br>
't' value can start from 0 but, i would like to know what value does<br>
gromacs use, more specifically for g_hbond.<br>
Can anyone help me? Thank you.<br>
<br>
Rama<br>
<br>
</blockquote></div></div>
The <> tell you that all time origins x are used, so<br>
C(t) = < f(x).f(x+t) >_x<br>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Postdoctoral Research Scholar,<br>Department of Chemistry,<br>University of Nevada, Reno.<br>