[gmx-users] S-type Hydrogen bond correlation function
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Nov 9 22:04:22 CET 2009
Ramachandran G wrote:
> I commented out the 'read_next_x' routine and in place of it i added
> 'read_next_frame' as given below will that work?
You could try it, but it won't work. The whole do...while loop needs to
be adjusted to use fr and its struct members, rather than separate box,
t, x, etc. Also read_first_frame is required before the loop, not
whatever is used there.
> Now if i install will i get the trajectory? Is API available for
> gromacs? Thank you.
Pre 4.1, API documentation is patchy at best. You can see how this
machinery gets used by comparing with the source code of a tool that
read and write non-position data, e.g. gmxdump and doubtless others.
Obviously, you'll need to recompile and re-install to use any new version.
Mark
> write_trx(out,natoms,swi,&top.atoms,0,t,box,x,NULL);
> }
> /* } while(read_next_x(status,&t,natoms,x,box)); */
> } while(read_next_frame(status,&fr));
> close_trj(status);
> if (out != -1)
> close_trx(out);
> if (fp)
> ffclose(fp);
>
> thanx(stderr);
>
> return 0;
> }
>
>
> On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> 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
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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!
>>>>>>>>>>>>>> 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!
>>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
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>>>>>>
>>>>>
>>>> _______________________________________________
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>>>
>>>
>> _______________________________________________
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