[gmx-users] S-type Hydrogen bond correlation function
David van der Spoel
spoel at xray.bmc.uu.se
Sun Nov 1 08:43:13 CET 2009
Ramachandran G wrote:
> Dear David,
> Thank you for you help. It is very much helpful for me.
>
> I have one more question. Is it possible to create index file for the
> oxygen atom or water molecules alone exist in a hydration shell. Thank
> you again.
> Rama
>
You could try the trjorder program
> On Wed, Oct 7, 2009 at 2:58 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>
>> 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
>>>>>>>> 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
>>>>>> _______________________________________________
>>>>>> 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!
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>>>>>> interface
>>>>>> or send it to gmx-users-request 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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