[gmx-users] S-type Hydrogen bond correlation function

[David van der Spoel]

Ramachandran G wrote:
>               C_HB(T)  =  <h(t)h(T+t)>/ <h(t)>
> 
>               S_HB(T)  =  <h(t)H(T+t)>/<h(t)>
> 
> 
>                    h(T)  =  1, if a pair of atoms bonded at time T,
>                           =  0, otherwise
> 
>                    H(T) = 1, if a pair of atoms continously bonded
> between time 0 to time T,
>                           = 0, otherwise
> 
> S_HB(t) probes the continuous existence of a hydrogen bond, while
> C_HB(t) allows for
> the reformation of a bond that is broken at some intermediate time. The former
> is thus a strict definition of the hydrogen bond lifetime, while the
> latter is more
> permissive.
> 
> I feel in gromacs, g_hbond does the C_HB(t). But i am not very sure
> about that. Anybody knows
> please help me. Thank you.
This is correct. However, the S_HB definition is not very useful, see my 
paper J. Phys. Chem. B. 110 pp. 4393-4398 (2006) for an explanation. The 
uninterrupted life time is computed by g_hbond however. Check the screen 
output.

> 
> Rama
> 
> On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> Ramachandran G wrote:
>>> Dear gromacs users:
>>>       I like to know whether gromacs will calculate S-type hydrogen
>>> bond correlation function?
>>> If it so how it can be done? Thank you.
>> What does that mean?
>>
>>
>>> Rama
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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.
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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