[gmx-users] S-type Hydrogen bond correlation function
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 3 06:41:59 CET 2009
Ramachandran G wrote:
> 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.
It seems likely to be straightforward to change the main loop of
gmx_trjorder to use read_next_frame, which will permit it to read and
write velocities and forces if they are present. I don't have time to do
it, though.
Mark
> 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
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> 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
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>>>>>>>>>>>>> posting!
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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!
>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>>> 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!
>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>> 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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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
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>>>
>>>
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