I created a MGDG membrane I want to know how can I calculate number of water molecules which create hydrogen bond with lipids per lipid. Gromacs can only calculate number of all hbonds between two groups, but one water molecule can make not only one hbond, but also two, so my value is a little bit higher. How can I also calculate a number of water bridges in the same lipid and between two different lipids?
Hi Jakub,
You can do that combining different gromacs commands. First, you have to create make index files of atoms or groups of interest using gmx make_ndx and then use basic commands: gmx distance and gmx analyze to calculate distances and probabilities of water bridges.
If you are looking for a way to do this where you aren't analyzing by your own code, you can easily do this in VMD. Extensions > Analysis > HBonds. Then you can select groups and also tell it to calculate residue pairs etc.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics