[gmx-users] Hydrogen bonding

[Justin A. Lemkul]

Sarah Witzke wrote:
> Dear gmx-users,
> 
> 
> 
> I have done simulations of one small molecule that diffuses into a DMPC
> membrane. This small molecule contains an alcohol group and is therefore
> capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol
> region).
> 
> I have read the manual (section 8.12 and g_hbond -h), searched the mailing
> list and google but I have not been able to find a more thorough description
> of the output possibilities than in the manual.
> 
> I have tried three different approaches:
> 
> 1. The -OH group of the small molecule and the glycerol oxygens
> 
> 2. The -OH group of the small molecule and the phosphate oxygens
> 
> 3. The small molecule and DMPC (no subgroups)
> 
> No. 1 gives 38 hbond, no. 2 gives 15 hbonds and no. 3 gives 53 hbonds. So 1 +
> 2 = 3, which is fine.
> 

I'm assuming this is just some theoretical limit that you have established, and 
not something that has actually been calculated, correct?

> 
> 
> Below is the output from no. 1: (gromacs 4.0.4)
> 
> Specify 2 groups to analyze:
> 
> Selected 0: 'O11_&_PALC_H12_&_PALC'
> 
> Selected 1: 'O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC'
> 
> Checking for overlap in atoms between O11_&_PALC_H12_&_PALC and
> O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC
> 
> Calculating hydrogen bonds between O11_&_PALC_H12_&_PALC (2 atoms) and
> O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC (384 atoms)
> 
> Found 1 donors and 385 acceptors
> 
> Making hbmap structure...done.
> 
> 
> 
> Will do grid-seach on 15x15x24 grid, rcut=0.35
> 
> Found 15 different hydrogen bonds in trajectory
> 
> Found 23 different atom-pairs within hydrogen bonding distance
> 
> Merging hbonds with Acceptor and Donor swapped
> 
> - Reduced number of hbonds from 15 to 15
> 
> - Reduced number of distances from 23 to 23
> 
> Average number of hbonds per timeframe 0.083 out of 192.5 possible
> 
> 
> 
> What does these "15 different hydrogen bond in trajectory" mean? I don't
> understand this. I also don't understand "Average number of hbonds per

That means quite literally what it says: there are 15 distinct hydrogen bonds 
that form at some point in your trajectory.  They are listed in hbond.ndx 
(output of -hbn) and mapped in hbmap.xpm (from -hbm).  You should find that 
there are 15 :)

> timeframe 0.083 out of 192.5 possible" - 192.5 possible hbonds?? Can anyone
> shed some light on this?

You have 385 H-bond acceptors (see the output above).  It appears that g_hbond 
makes a simple assumption that if half of these were occupied (with the other 
half of the group serving as a donor, which may or may not ever have any 
physical significance), then the maximum number of H-bonds would be 385/2 = 192.5.

The average printed is simply the average number of H-bonds that are present 
between your two groups at any given time.  If your small molecule has only one 
-OH group that you're considering, the maximum number of H-bonds per timeframe is 1.

> 
> 
> 
> Another question relates to the lifetime of the hbond calculated when the
> "-life" flag is given. The produced .xvg file contain three columns: time,
> p(t), and t p(t). What is p(t) and t p(t)? And how can I find the lifetime?
> 
> 

The explanation is probably in one of the "Please read and cite the following 
reference" messages that g_hbond spits out.  Looks like some sort of probability 
function.  You should also be cautioned by this warning from using the -life option:

"Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime"

-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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