[gmx-users] g_hbond output analysis

[David van der Spoel]

parthiban at ncbs.res.in wrote:
>> Message: 1
>> Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST)
>> From: parthiban at ncbs.res.in
>> Subject: [gmx-users] g_hbond output analysis
>> To: gmx-users at gromacs.org
>> Message-ID: <56573.192.168.1.1.1219745336.squirrel at mail.ncbs.res.in>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> hi
>>
>> i used the -num option for g_hbond run. since i new to gromacs i cannot
>> able to interpret the output form. it comes in 3 columns with the first
>> column indicating the frame, i dont know about the remaining two columns
>>
>> Kindly suggest
>>
>> Parthiban & sundar
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 26 Aug 2008 12:13:55 +0200
>> From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
>> Subject: Re: [gmx-users] g_hbond output analysis
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <200808261213.57421.Florian.Haberl at chemie.uni-erlangen.de>
>> Content-Type: text/plain;	charset="utf-8"
>>
>> Hi,
>>
>> On Tuesday, 26. August 2008, parthiban at ncbs.res.in wrote:
>>> hi
>>>
>>> i used the -num option for g_hbond run. since i new to gromacs i cannot
>>> able to interpret the output form. it comes in 3 columns with the first
>>> column indicating the frame, i dont know about the remaining two columns
>> if you use
>>
>> g_hbond -h it tells you also if you have the legend inside the file (do
>> not
>> select -noxvgr)
>>
>> 2: Hydrogen bonds
>> 3: Pairs within 0.35nm (depends on your select cutoff radius)
>>
>>
>>
>>> Kindly suggest
>>>
>>> Parthiban & sundar
>>>
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>>
>> greetings,
>>
>> Florian
>>
>> --
>> -------------------------------------------------------------------------------
>>  Florian Haberl
>>  Computer-Chemie-Centrum
>>  Universitaet Erlangen/ Nuernberg
>>  Naegelsbachstr 25
>>  D-91052 Erlangen
>>  Telephone:  	+49(0) − 9131 − 85 26573
>>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>> -------------------------------------------------------------------------------
> 
> Dear Florian & other users
> 
> can you pls. explain me in detail about the 3rd column in the g_hbond
> output in -num option
it is the number of contacts, within the distance cut-off but not 
h-bonded. this is used in the HB kinetics analysis.

> 
> Parthi & sundar
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se