[gmx-users] S-type Hydrogen bond correlation function
Ramachandran G
gtrama at gmail.com
Tue Nov 3 04:25:49 CET 2009
Yes, i do write velocities to output trajectory at 10 fs. But i
understood from the thread(below link)
that 'trjorder' do not save the velocities....
http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html
I don't know is there any other way we can do it in the new version.
Thanks.
Rama
On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Ramachandran G wrote:
>>
>> 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.
>
> First, your .mdp must specify the recording of velocities. Then consult the
> documentation for trjorder and g_velacc for what you want.
>
> Mark
>
>> 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
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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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>>>>>
>>>>>
>>>>
>>>>
>>>>
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>>
>>
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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