[gmx-users] H-bonds

Mr Bernard Ramos bgrquantum at yahoo.com
Wed Feb 1 11:28:23 CET 2012

Hi everyone!

I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru H-bonds, I noticed that g_hbond does not seem to give consistent results. As previously discussed in this list, I am taking advantage of the hbmap file to parse out the Hbond trajectories needed to count the water bridges. A possible water-bridge type is one in which the hydrogen of a water molecule is shared by two different oxygens of the solute. Since there are two H's per water molecule I expected two sets of indices for each H. This is what I did.

1. To simplify parsing the resulting HBMap, I intended to create an HBMap.xpm for a water and a pair of hydroxyl residues from the solute. For a shared H above, that would be (O solute...Hwater...O solute). Creating a set of indices for this configuration was successful upon running (g_hbond .... -hbn), but only for one set of Hwater. g_hbond was not able to create another set for the other H of water. (Note though that g_hbond was able to correctly identify both Hs of water as donors). g_hbond correctly counted H-bonds for this set and produced a reliable HBMap.xpm 

2. Another set of indices was manually created for the other H. However, the hbnum.xvg of this set is unreliable compared with the above and the values shoot to 1000 times expected h-bond counts. Please note that the HBMap.xpm for the hydrogen bonds between water and the solute only lists one H for each water as if ignoring the other H (in cases that there should be two). 

Your advice/ideas/comments is very much welcome and very much needed.


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