[gmx-users] -don (g-hbond)

atila petrosian atila.petrosian at gmail.com
Wed Nov 10 14:32:53 CET 2010

Dear Justin

I confused.
number of donors in donor.xvg file is 203.  while, when use g_hbond: found
143 donors.

Select a group: 2
Selected 2: 'Protein_A'
Select a group: 3
Selected 3: 'Protein_B'
Checking for overlap in atoms between Protein_A and Protein_B
Calculating hydrogen bonds between Protein_A (1042 atoms) and Protein_B (825
Found 143 donors and 439 acceptors
Making hbmap structure...done.
Reading frame       0 time 19500.000
Will do grid-seach on 14x14x14 grid, rcut=0.35
Reading frame     120 time 19980.000
Found 40 different hydrogen bonds in trajectory
Found 69 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 40 to 40
- Reduced number of distances from 69 to 69
Average number of hbonds per timeframe 19.310 out of 31388.5 possible
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