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

[Ramachandran G]

              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.

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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>
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Department of Chemistry,
University of Nevada, Reno.