[gmx-users] Re: g_hbond output
Jianguo Li
ljggmx at yahoo.com.sg
Wed Mar 16 10:25:46 CET 2011
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 <lnzhao99 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at 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 <ljggmx at 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 <lnzhao99 at gmail.com>
>To: Discussion list for GROMACS users <gmx-users at 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 at 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-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110316/e1547e67/attachment.html>
More information about the gromacs.org_gmx-users
mailing list