[gmx-users] Hydrogen bonding

Sarah Witzke sawit02 at student.sdu.dk
Wed Nov 18 00:23:48 CET 2009

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.


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


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?


Thank you in advance,


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