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

[David van der Spoel]

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
> <spoel at 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
>>> <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.
>>>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>>> _______________________________________________
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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
>> _______________________________________________
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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