A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, but cannot belong to both columns.
If the program finds a pair shorter than 0.35nm, and the angle is smaller than 30deg., then the program put this pair in the column 2. If the program finds a pair shorter than 0.35nm, and the angle is larger than 30deg., then the program put this pair in the column 3. Jianguo ________________________________ From: ZHAO Lina <lnzha...@gmail.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wednesday, 16 March 2011 15:31:30 Subject: Re: [gmx-users] Re: g_hbond output s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 Here is my question, since there is already one bond formed, then why there is none pairs in 1000? On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li <ljg...@yahoo.com.sg> wrote: If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. >Jianguo > > > ________________________________ From: ZHAO Lina <lnzha...@gmail.com> >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Sent: Wednesday, 16 March 2011 13:33:57 >Subject: [gmx-users] Re: g_hbond output > > >@ legend length 2 >@ s0 legend "Hydrogen bonds" >@ s1 legend "Pairs within 0.35 nm" > 0 0 0 > 200 0 0 > 400 2 1 > 600 0 3 > 800 0 2 > 1000 1 0 > : > 50000 3 2 > >Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the >$3 >means pairs. > >I tried pymol, and on the last frame, >there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 > >Thanks and sorry for last email without my realization it sent. > >lina > > >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search >before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists