[gmx-users] S-type Hydrogen bond correlation function
Ramachandran G
gtrama at gmail.com
Sun Nov 1 08:09:06 CET 2009
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
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
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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
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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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>
--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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