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Bug #149

-[no]da flag in g_hbond is broken

Added by Erik Marklund over 12 years ago. Updated about 12 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

-[no]da doesn't work. The two following commands generate identical results:
g_hbond ... -noda -r 0.25
g_hbond ... -da -r 0.25
It seems the donor acceptor distance is used at all times. The same problem
arises in gmx 3.3, 3.3.2b and in the 4.0 development code.

grompp_run.tpr (2.2 MB) grompp_run.tpr tpr-file matching short.xtc Erik Marklund, 09/11/2007 12:33 PM
short.xtc (5.12 MB) short.xtc trajectory mathing grompp_run.tpr Erik Marklund, 09/11/2007 12:34 PM
short.xtc (5.12 MB) short.xtc trajectory mathing grompp_run.tpr Erik Marklund, 09/11/2007 12:37 PM

History

#1 Updated by David van der Spoel about 12 years ago

Can you please supply an example with command line etc.

#2 Updated by Erik Marklund about 12 years ago

Created an attachment (id=229)
tpr-file matching short.xtc

tpr-file from gmx 4.0

#3 Updated by Erik Marklund about 12 years ago

Created an attachment (id=230)
trajectory mathing grompp_run.tpr

#4 Updated by Erik Marklund about 12 years ago

Created an attachment (id=231)
trajectory mathing grompp_run.tpr

#5 Updated by Erik Marklund about 12 years ago

Oops, uploaded trajectory twice.

commandline:
g_hbond -s grompp_run.tpr -f short.xtc -num da_num -g da_g -da
g_hbond -s grompp_run.tpr -f short.xtc -num noda_num -g noda_g -noda

da_num.xvg and noda_num.xvg were identical, apart from comments/quotes. It was all done with gmx version 4.0 and the AMBER03 force field.

#6 Updated by David van der Spoel about 12 years ago

Fixed in CVS.

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