[gmx-users] intrapeptide hbond existence map

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Feb 11 17:00:26 CET 2010

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 


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


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