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
<sp...@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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