SV: SV: SV: [gmx-users] Hydrogen bonding

[Sarah Witzke]

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Thu 19-11-2009 02:09
To: Gromacs Users' List
Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding
 

Sarah Witzke wrote:
>  
> 
> Sarah Witzke wrote:
> 
> <snip>
> 
>> ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps?
>>
> 
> Yes, per the calculation.  For a bit more about the analysis, see the "Please
> read and cite" notices, as well as this thread:
> 
> http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html
> 
>> The note about the correlation function would imply that the correlation
>> function itself has not converged until its value is < 0.001.  This is usually a
>> result of insufficient data, either the length of the simulation, or number of
>> frames analyzed (based on the spacing of the frames).
>>
>> Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) is not long enough. Perhabs I should try the original .trr file... The .xtc file I'm using only contains DMPC and the small molecule, no solvent - I can't see this would make a difference in this case, am I right?
>>
> 
> The correlation will depend on how much the interactions are changing over the
> period you analyzed.  If you are analyzing a small molecule and DMPC, water
> should not matter.
> 
> I have now tried with the full length (220 ns) .trr file and the -ac output still prints a warning:
> 
>   ACF 106/106
>   Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05
> 
>   WARNING: Correlation function is probably not long enough
>   because the standard deviation in the tail of C(t) > 0.001
>   Tail value (average C(t) over second half of acf): 0.000172327 +/- 0.00277407
> 
> In your opinion, does this mean that I cannot trust the value of the lifetime, since the correlation function is not converging?
> 

  I'm not entirely sure.  Please see the posts from David in the thread I
  referenced before about some potential issues with the ACF in the g_hbond
  calculation.  I assume you are using version 4.0.x?

I'm using version 4.0.4 for consistency. I have read the posts from you and David van der Spoel (http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html) as well as the article given by g_hbond. I guess this auto correlation function and the lifetime derived by this is... well, I'm not sure I trust it enough to put it in a paper - especially since my acf doesn't converge (which I still find strange, it should not matter that I have only saved coordinates every 10 ps in my .trr file when using the Luzar acfs-approached, right?). 

The - hbm option i g_hbond creates a matrix that can be converted to a .eps file by usin xpm2ps. The picture obtained is nice looking but lacking in some of the information I would like to derive. I would like to know how many frames each hbond exists (another way to consider lifetime). I have opened the .xpm file in a text editor and there are a long list of lines starting similar to tgis one: 
  /* x-axis:  100000 100010 100020 
Can I somehow obtain the number of frames for each hbond from this?

Thank you very much again!

-Justin

> Thank you!
> 
> 
> I have conducted the analysis on the 
> -Justin
> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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