[gmx-users] Interpretation of g_hbond results

[Manik Mayur]

On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul <jalemkul at vt.edu> 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?

--------------------------------------------------
> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090225/10f3e0dc/attachment.html>