Re: [gmx-users] g_hbond -contact option

2006-11-23 Thread Yang Ye 
Besides used for h-bond, g_hbond can be used for determine whether the 
distance has fallen into a range (with -nocontact and -r and -r2).


g_dist is not good for calculate for distance between two atoms but 
g_mindist can perform this job well. Actually, because of a compulsive 
input of tpr file, g_dist has less use than g_mindist when coming to 
mere distance calculation.


Regards,
Yang Ye

On 11/22/2006 5:46 PM, andrea carotti wrote:

Hi all,
I have found this interesting option in g_hbond, and I would like to
know something more about it. How does it work? Which is the difference
with other tools like g_dist?
Thanks to all
Andrea

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Re: [gmx-users] g_hbond -contact option

2006-11-22 Thread Erik Marklund 
If I'm not mistaken, g_dist deals with the center of mass of the two groups 
chosen, whilst g_hbond -contact is all about the distances of individual 
atoms of the two/one group(s). g_hbond -contact works just like g_hbond, 
except that it ignores the angle criterion for hydrogen bonds. You can also 
provide a second distance using the -r2 option, assuming a two step 
interaction process. I strongly suggest using the latest version of gromacs 
when using g_hbond -contact, since there were a bunch of bugfixes made not 
too long ago.


/Erik Marklund

- Original Message - 
From: andrea carotti [EMAIL PROTECTED]

To: gmx-users@gromacs.org
Sent: Wednesday, November 22, 2006 10:46 AM
Subject: [gmx-users] g_hbond -contact option



Hi all,
I have found this interesting option in g_hbond, and I would like to
know something more about it. How does it work? Which is the difference
with other tools like g_dist?
Thanks to all
Andrea

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