[gmx-users] gmx hbond

[Mohsen Ramezanpour]

Thanks Erik, It helped.

Cheers

On Sat, Apr 15, 2017 at 9:30 AM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> 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
> ______________________________________________
> 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
> change.
>
>
> 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
> 0.30
>
> 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
> either.
>
> 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
> Cheers
> Mohsen
>
>
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*Rewards work better than punishment ...*