[gmx-users] gmx hbond

Erik Marklund erik.marklund at kemi.uu.se
Sat Apr 15 17:31:01 CEST 2017

Dear Moshen,

I doubt the difference in versions will cause any problems in this case.

The second column is ill-described. It contains the number of pairs within 0.3 nm that don’t fulfil the angle criterion.

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 14 Apr 2017, at 03:20, Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com<mailto:ramezanpour.mohsen at gmail.com>> wrote:

Hi Gromacs users,

I have a question regarding the output file from g_hbond:

First:I have done my simulations with version 4.6.7 and doing the analysis
with version 2016.2
Will this cause any hidden problem in analysis? the analysis is working
fine but I am asking about the correctness of results because of this

Second and the main question:

When I use this command:
gmx hbond -f md.xtc -n index.ndx -s  file.tpr -num hbond.xvg -g test.log -r

I get this:

@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.3 nm"
       40            0           0
*      40.1           1           0*
     40.2           1           3
     40.3           2           2
     40.4           0           2
     40.5           1           1
*      40.6           2           0*
the first column is time frame
the second is number of h-bonds
the third is "Pairs within 0.3 nm"

by -r 0.30 I wanted to change the cut-off for h-bond definition.
i.e. report a h-bond if and only if the D...A distance is less or equal to
0.30 ns, AND, the angle of H..D...A is less or equal than 35 (this angle is
default in 2016.2 version).

Regarding the highlighted lines:
How it is possible that the there is not any pair in this distance but we
still have hbond?
If they are not in this cut-off, thy should not be recognized as hbond

I assume the pair means the D...A pair because I did NOT use -noda  option.

Also, it does not give any test.log file, and other problems :-)

Please let me know your opinion about this results.

Thanks in advance for your reply

*Rewards work better than punishment ...*
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