[gmx-users] g_hbond range checking error

[Dallas B. Warren]

Upgraded it to 3.3.1 now, still get the same error ...

Using this command:
############################
g_hbond -f ../76.55-78.95ns.xtc -s ../md_000.tpr -n index.ndx -num
hbnum_MGL-MGL
############################
 
I get this output:
############################
Reading file ../md_000.tpr, VERSION 3.2 (single precision)
Note: tpx file_version 31, software version 40
Specify 2 groups to analyze:
Group     0 (         DGL) has 158400 elements
Group     1 (         MGL) has 100800 elements
Group     2 (     DGL_MGL) has 259200 elements
Select a group: 1
Selected 1: 'MGL'
Select a group: 1
Selected 1: 'MGL'
Calculating hydrogen bonds in MGL (100800 atoms)
Found 9600 donors and 19200 acceptors
Reading frame       0 time 76550.000
Will do grid-seach on 44x46x52 grid, rcut=0.35
-------------------------------------------------------
Program g_hbond, VERSION 3.3.1
Source code file: gmx_hbond.c, line: 669

Range checking error:
Variable gx has value -24. It should have been within [ 0 .. 44 ] Please
report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
############################

Note, when running the script on the other group in the list, DGL, the
error does not occur.  However, it takes a very long time under the
grid-search process.  Not sure whether that should be the case or not
with this number of atoms involved or not.  I actually left it running
for three days and it was still churning away at it with no change to
the display.

Would it help if in the groups I simply narrowed the index file down to
just the atoms that will be involved in the H-bonding?  And leave out
all the ones the don't?  No idea how it handles all the atom lists, so
not sure if that will help reduced load or not.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
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a nail.