Manik Mayur wrote:
On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Hi,
I have a quick question about interpreting the output from g_hbond.
I am using the -ac option to calculate H-bond lifetimes between my
protein and a series of different, bound ligands. I read the
associated paper, but I would like to confirm the interpretation of
the results before I continue much further. I obtained the following:
Which paper are you talking about? Is there a paper for each gromacs
postprocessing tool?
Look for this type of information in the output (either to screen or to logs in
the case of mdrun):
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------
I don't know if there is a paper for every single tool, but pertinent algorithms
are cited when necessary.
-Justin
--------------------------------------------------
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.003 309.475 19.590 0.000294756
Backward 0.007 136.034 17.471
One-way 0.002 471.990 20.678
Integral 0.001 1534.894 23.717
Relaxation 0.002 606.619 21.325
The "forward" and "backward" rates and times make sense based on
equations 3 & 4 in the paper, but I could not find an explanation of
what "one-way" and "relaxation" are. Is the "integral" value taken
from equation 2, and thus should be interpreted as the overall
H-bond lifetime?
Thanks,
Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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