[gmx-users] S-type Hydrogen bond correlation function
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 3 03:36:24 CET 2009
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
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>> 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.
>>>>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> --
>>>>>>>> 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.
>>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> 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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>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>>>
>>>>>
>>>> --
>>>> 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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>>>>
>>>>
>>>
>>>
>>>
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