[gmx-users] S-type Hydrogen bond correlation function
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 7 11:58:05 CEST 2009
Ramachandran G wrote:
> I have used the option as follows:
> g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg
-life koko.xvg
>
> To find the continious HB-correlation function, what option should i
> need to use.
> Thank you for your help.
> Rama
>
> On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> 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
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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