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

[Ramachandran G]

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:

-----------------------------------------------------------------------------------------------------------------------------------------
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
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>> --
>>> 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
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>
>
> --
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.