Ramachandran G wrote:
Thank you for the reference. But still i like check it out for my
system. But still i don't know how to get 'S' type hydrogen bonding.
I am pasting my screen output below:
You need to pass the -life option.
-----------------------------------------------------------------------------------------------------------------------------------------
Checking for overlap in atoms between plane-B and SOL
Calculating hydrogen bonds between plane-B (434 atoms) and SOL (33036 atoms)
Found 6650 donors and 19904 acceptors
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Will do grid-seach on 16x16x16 grid, rcut=0.35
Last frame 30000 time 300.000
Found 3304 different hydrogen bonds in trajectory
Found 7135 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
6650/6650
- Reduced number of hbonds from 3304 to 3151
- Reduced number of distances from 7135 to 7135
Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2#
Average number of hbonds per timeframe 98.421 out of 6.61808e+07 possible
ACF 3151/3151
Normalization for c(t) = 0.0101617 for gh(t) = 3.38722e-07
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001
Tail value (average C(t) over second half of acf): 0.124513 +/- 0.0254161
Hydrogen bond thermodynamics at T = 298.15 K
--------------------------------------------------
Type Rate (1/ps) Time (ps) DG (kJ/mol)
Forward 0.035 28.458 12.829
Backward -0.009 -111.540 -666.000
One-way 0.074 13.435 10.968
Integral 0.047 21.471 12.130
Relaxation 0.047 21.358 12.117
gcq#129: "She's a Good Sheila Bruce" (Monty Python)
-----------------------------------------------------------------------------------------------------------------------------------------------
The hydrogen bond Autocorrelation function output has five columns.
The first columne is the time axis,
i think the second column gives the C(t) other 3 columns i don't
understand. Will you please help me to understand thank you.
Rama
On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
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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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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