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Bug #88

g_hbond termodynamics unsing -contact -ac

Added by Erik Marklund over 13 years ago. Updated over 13 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

The forward and backwards rate constants calculated using -ac normally refer to
the reaction A <=> B where A is 'h-bonded' and B is 'within cut-off but not
h-bonded'. The -contact option causes this description to fail since A then is
defined as 'contacts (= within cut-off)' and B is ... well, what is B really?
One way of solving this problem is to define a second, larger cut-off R2,
defining A = 'within cut-off R' and B = 'within cut-off R2'. If R2 is undefined
one could simply redefine B = !A. I recommend reading Luzar 2000 for
theoretical background.

I intend to fix this bug myself as soon as possible, since I need this feature
to work for a paper I'm currently working on. Hopefully it's done in a week (I'm
fairly familiar with the code by now), otherwise it'll probably have to wait
until the end of july/beginning of august. My strategy is to introduce yet
another array in the t_hbond structure containing contacts within R2 (see above)
when -R2 and -contact options are set. If -R2 is not provided I'll define B = !A
as described above. -R2 will certainly demand more memory, but hey, what can you do?

Erik Marklund, PhD student
ICM, Molecular Biophysics group
Uppsala University

History

#1 Updated by Erik Marklund over 13 years ago

Bug fixed about a month ago. I forgot to change its bugzilla status, however.
Sorry about that.

Erik Marklund, PhD student
ICM, Molecular Biophysics group
Uppsala University

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