<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2900.2912" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>Having recently made a bunch of changes in g_hbond
(and comitted it to the cvs repository), I have discovered that the -ac
option still isn't working properly in conjunction with the -contact option. The
problem is not just a programming error, but actually insuficient
theory/phonomenology. When analyzing h-bonds everything is fine. Forward and
back rate constants are calculated for the reaction A <=> B, where A =
'h-bonded' and B = 'within cut-off but not h-bonded'. For contacts, however, A
is 'within cut-off range R', but how should B be defined? One possibility is
to use B = !A, which doesn't follow the theory being
described in Luzar 2000 and that is used in the present code for h-bonds.
Another possibility is to define a second cut-off range R2 and say that B =
'within R2, but not within R'.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I have posted a bugzilla (#88) and hope to resolve
this issue all by myself this week. However, any suggestions or wise comments
are more than welcome. This is the stratregy I have decided to go
for:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>- introduce option -R2, being the second cut-off
(see above)</FONT></DIV>
<DIV><FONT face=Arial size=2>- add an additional array to the t_hbond structure
containing contacts within R2, similar to g[] (see code).</FONT></DIV>
<DIV><FONT face=Arial size=2>- if -R2 is positive and -contact and -ac flags are
set, calculate the autocorrelation stuff using the second definition of B
above.</FONT></DIV>
<DIV><FONT face=Arial size=2>- if R2 is zero, B is defined as !A and the
autocorrelation stuff is calculated accordingly.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Using -R2 will obviously require more memory.
Hopefully this will not be a big problem.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>When done I will of course commit these new
features/bugfixes to the cvs repository. And as I mentioned previously I'll be
glad to recieve suggestions and comments, but please send them soon, for
I'll go on vacation this sunday.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>/Erik Marklund</FONT></DIV>
<DIV>-- <BR>Erik Marklund, PhD Student, Molecular Biopcysics group,<BR>Dept. of
Cell and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box
596, 75124 Uppsala,
Sweden<BR>phone: 46 18 471
4537 fax: 46 18 511
755<BR><A href="">erikm@xray.bmc.uu.se</A><BR></DIV></BODY></HTML>