[gmx-users] S-type Hydrogen bond correlation function
Ramachandran G
gtrama at gmail.com
Wed Oct 7 09:36:45 CEST 2009
I have used the option as follows:
g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.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
>>> _______________________________________________
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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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> Please search the archive at http://www.gromacs.org/search before posting!
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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