[gmx-users] intrapeptide hbond existence map

[Ran Friedman]

Hi Stephane,

The map shows weather a certain hydrogen bond exists at a certain time.
In principle you can get the information by integrating this data, but
I'm not sure it can be done without changing the code. A possible
solution is to use a script and run g_hbond -num 28 times with two
relevant groups (N-H  donor and oxygen acceptor), and calculate the
occupancy based on this (I guess you mean the fraction of time that this
h_bond existed.

Ran.

ABEL Stephane 175950 wrote:
> Hi everybody, 
>
> I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water 
>
> I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this 
>
> NH--CO
>
>
> [intra_hbds]
> 4 17 5
> 18 26 19
> 27 43 28
> 44 52 45
> 53 60 54
> ....
>
> to obtain the INTRHB existence map i used the command with gmx4.05
>
> g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 400000 -e 500000 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map
>
> The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg
>
> I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 
>
> Thank you in advance for your help
>
> Stephane
>