[gmx-users] H-Bond lifetimes and free energies in 4.5.6

Cara Kreck cara_a_k at hotmail.com
Fri Jan 10 03:58:18 CET 2014

I've calculated H-Bond lifetimes and free energies of activation for several different water models and found that they don't agree with the values reported in David van der Spoel's JPCB 2006 paper. I also found unrealistically high Nfree values in the nhbdist.xvg file when I was trying to calculate the free energy of bonding . I then stumbled across this old post:
>>> Two caveats: first, we recently found out that the numbers in my JPCB 
>>> paper can not be reproduced in 4.0 (embarassingly this was found out 
>>> during a tutorial that I was giving). We are looking into this. Second 
>>> we are busy implementing a new algorithm due to Markovitch * Agmon 
>>> (JCP 129 (2008) p. 084505) that has several advantages over the Luzar 
>>> approach.
>> My simulations were conducted under 4.0.2, should I not use these 
>> results? Results from 3.3.x should be correct, since it was used in your 
>> JPCB paper; but my installation of 3.3.3 gives a segmentation fault on 
>> our cluster, and a bus error on my local machine.  Are there known 
>> issues with g_hbond-3.3.3?
>As said, we are looking into this. With the original trajectories from 
>the paper the 4.0 code gives different values. I haven't tried with 3.3 
>analysis tools yet. Digging back into my memory, the problem seems to 
>have to do with the correlation function rather than the analysis, that 
>is, you can do the Luzar analysis in xmgrace. based on the ACF that 
>g_hboond spits out. If you do so you find that you get the same results 
>as g_hbond prints, ergo the Luzar analysis is implemented OK, but the 
>ACF is suspect. 
I just wanted to check if this has been resolved or if there is an issue that has persisted to the 4.5.6 and 4.6.1 versions of the code. Unless it was discovered that the problem was actually with the older code, it looks like the newer versions are still wrong.

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