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
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