[gmx-users] S-type Hydrogen bond correlation function
Ramachandran G
gtrama at gmail.com
Mon Nov 9 21:30:10 CET 2009
I commented out the 'read_next_x' routine and in place of it i added
'read_next_frame' as given below will that work?
Now if i install will i get the trajectory? Is API available for
gromacs? Thank you.
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
>>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>>>>>>> Please search the archive at http://www.gromacs.org/search
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>>>>>>>>>>>>>> Can't post? Read
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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!
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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
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
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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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