Bug #62

g_hbond problem

Added by Jonathan Moore over 14 years ago. Updated over 14 years ago.

analysis tools
Target version:
Affected version - extra info:
Affected version:


I created a hydrogen bond map using g_hbond of version 3.3. The manual
indicates that for the hbmap the "Ordering is identical to that in -hbn index
file." However, in my case, the hbmap file contains 13 hydrogen bond indices,
but the hbond.ndx file lists 20 sets of donors and acceptors. Thus, I don't
know how to determine which specific hydrogen bonds are represented in the
hbmap data. Another user suggested that the hbonds that actually occur are
listed in the log file, but I could not get a log file to write (see other
g_hbond bug submission by me).


#1 Updated by David van der Spoel over 14 years ago

Please upload trajectory (short) tpr and command line to reproduce the problem.

#2 Updated by Jonathan Moore over 14 years ago

(In reply to comment #1)

I figured out what the difficulty is. I used a command like:
g_hbond -f filename -s filename -num -hbn -hbm -n index.ndx

Thus, I was using the default -merge option. For the particular case I was
running, there are 41 hbonds listed in the outputted hbond.ndx file but only
30 listed in the outputted hbmap file. I just noticed in the g_hbond output
that 30 is the number of hbonds that result after merging hbonds with donor
and acceptor swapped. So, I guess I could go through the 41 hbonds listed in
hbond.ndx and throw out each of the second occurrences with donor and acceptor
swapped, and that should then leave the identities of the hbonds listed in the
hbmap file. However, I think it would be preferable to have a more
straightforward method to determine the hbond identities. Maybe include in
hbond.ndx a listing of hbonds after merging hbonds with donor and acceptor
swapped and leaving off the index number of the H? Or, I could use the -
nomerge option and handle the merging myself later.

#3 Updated by Erik Marklund over 14 years ago

Fixed this problem, along with -contact functionality and bugs in -ac -life -hbm.

/Erik Marklund, June 15

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