H-Bond measurements

From: Stephan Grein (grein_at_informatik.uni-frankfurt.de)
Date: Thu Aug 14 2014 - 01:57:40 CDT

Dear NAMD users,

I'm trying to measure some H-Bond distances (10 to 20) within a protein
of interest.
Therefore i ran a classical MD simulations (some timesteps, 5000) with a
protein of interest within a waterbox (PBC used). Then i evaluated the
distances by
the following script (where i have multiple donors and acceptors defined
as two lists of integers previously):

# puts "Selecting atom pairs"
set mysel1 [atomselect top "index [lindex $donor $j]"]
set mysel2 [atomselect top "index [lindex $acceptor $j]"]

# puts "Determing atom pairs coordinates for bond length measurement"
set coordinates1 [measure center $mysel1]
set coordinates2 [measure center $mysel2]

# puts "Measure length actually"
set mylength [vecdist $coordinates1 $coordinates2]

# puts "Delete representations since they consume too much memory within
a for loop"
$mysel1 delete
$mysel2 delete

Nevertheless I arrive at very long H-Bond distances (range from 0 to 50
Angström, actually does
vecdist return Angström?)

Is there in your opinion anything wrong with my code above?
I might attach also the namd configuration file for the MD simulations

Hope you can help me,
best regards,

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