[gmx-users] S-type Hydrogen bond correlation function
Ramachandran G
gtrama at gmail.com
Tue Nov 3 02:22:40 CET 2009
Thank you, I have installed new version of gromacs4.0.5 and trjorder
works fine in giving me the trajectory file(ordered.trr) but using
this file when i try g_velacc(velocity autocorrelation function) for
the water molecules, i am getting the result 'nan 0.000'. Later
when i checked the trajectory file(ordered.trr) by converting to *.gro
file using trjconv, i understood that 'velocities' are missing.
So, can you guide me how i can do velocity auto correlation function
for the water molecules exist close to the protein(i.e., in a
hydration shell) using gromacs? Thank you again.
Regards,
Rama
On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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
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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
>>> _______________________________________________
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>>>
>>
>>
>>
>>
>
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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