[gmx-users] Re: rotational correlation function
David van der Spoel
spoel at xray.bmc.uu.se
Fri Sep 24 10:39:08 CEST 2010
On 2010-09-23 21.10, Paymon Pirzadeh wrote:
> OK, To summurize:
>
> 1. I calculate the Ctot(t) with g_rotacf using N-H index files.
>
> 2. Use trjconv to get a trajectory of internal motions.
> => How I get the Cint(t)???
>
> 3. Crot = Ctot/Cint
>
> But, is there any way to calculate the Crot(t) directly? Is trjconv the
> solution again?
No and no.
Maybe when you use the -debug option to trjconv it spits out the
rotation matrix but I'm not sure.
Anyway you need to start trying things out from here.
> regards,
>
> Paymon
>
>
>
>
>
>
>
>
> On Thu, 2010-09-23 at 20:40 +0200, David van der Spoel wrote:
>> On 2010-09-23 20.38, Paymon Pirzadeh wrote:
>>> Great tips and advices. I appreciate your attention.
>>> But, what would the g_rms -fit rot+trans do?
>>
>> compute the rmsd. something different. I said trjconv.
>>>
>>> Paymon
>>>
>>>
>>>
>>> On Thu, 2010-09-23 at 20:07 +0200, David van der Spoel wrote:
>>>> On 2010-09-23 18.14, Paymon Pirzadeh wrote:
>>>>> Dear Dr. van der Spoel,
>>>>> Thanks a lot for your clarification. But some questions yet:
>>>>>
>>>>> 1. If I do not provide the "-aver" option, will the program calculate
>>>>> the C(t) for individual N-H bond?
>>>>>
>>>> Yes.
>>>>
>>>>> 2. In a paper that I just read, JCP vol. 131 155103 (2009), they claim
>>>>> they have calculated the Ctot(t) which could be factorized into
>>>>> rotational and internal components, Ctot(t)=Crot(t)*Cint(t). I assume
>>>>> g_rotacf gives the rotational part. How one can calculate the Ctot(t)
>>>>> (they claim they calculatetd the Ctot and Crot with GROMACS utilities)?
>>>>> How can we generate the rotation matrix (omega(t)) and use it? What's
>>>>> the use of "-fitfn"? Is it sth that could be done in other data
>>>>> processing softwares?
>>>> If your sim is long enough (10-20 times the rotation time, which for a
>>>> small protein is on the order of a couple of ns) you can fit all the
>>>> individual NH -acfs to two exponentials, 1 for the NH relaxation and one
>>>> for the overall.
>>>>
>>>>>
>>>>> 3. How can we generate a trajectory with no internal motions? Does it
>>>>> have anything to do with g_rms?
>>>> You can do the reverse by fitting trjconv -fit rot+trans this will give
>>>> you a protein with no overall rotation+translation from which you can
>>>> derive the order parameters and relaxation times of individual NH vectors.
>>>>
>>>>
>>>> Check this ref too:
>>>> @Article{Villa2006a,
>>>> author = {A. Villa and G. Stock},
>>>> title = {What NMR relaxation can tell us about the internal motion
>>>> of an RNA
>>>> hairpin: A molecular dynamics simulation study},
>>>> journal = {J. Chem. Theory Comput.},
>>>> volume = {2},
>>>> year = {2006},
>>>> pages = {1228-1236},
>>>> }
>>>>
>>>>>
>>>>> Sorry for mass of questions.
>>>>> Regards,
>>>>>
>>>>> Paymon
>>>>>
>>>>>
>>>>> On Thu, 2010-09-23 at 08:20 +0200, David van der Spoel wrote:
>>>>>> On 2010-09-23 01.27, Paymon Pirzadeh wrote:
>>>>>>> Dear Dr. Chaban,
>>>>>>> I meant the N-H bond vectors of protein backbone for calculation of
>>>>>>> rotational time correlation function to calculate the rotational
>>>>>>> diffusion constant of my protein. I need a protocol which walks me step
>>>>>>> by step through the procedure.
>>>>>>> Thanks for your Attention.
>>>>>> define all NH bonds in an index file as
>>>>>> [ NH ]
>>>>>> 5 6
>>>>>> 10 11
>>>>>> 23 24
>>>>>>
>>>>>> etc.
>>>>>>
>>>>>> Then run g_rotacf -P 2 [ more flags ] -aver
>>>>>> Analyze the ACF to extract the order parameters.
>>>>>> You will need to read Lipari& Szabo papers:
>>>>>> @Article{ Lipari82a,
>>>>>> author = "G. Lipari and A. Szabo and R. M. Levy",
>>>>>> title = "Protein Dynamics and {NMR} relaxation: comparison of
>>>>>> simulations with experiment",
>>>>>> journal = BTnature,
>>>>>> year = 1982,
>>>>>> volume = 300,
>>>>>> pages = "197-198"
>>>>>> }
>>>>>>
>>>>>> @Article{ Lipari82b,
>>>>>> author = "G. Lipari and A. Szabo",
>>>>>> title = "Model-Free Approach to the Interpretation of Nuclear
>>>>>> Magnetic Resonance Relaxation in
>>>>>> Macromolecules. 1. Theory and Range of Validity",
>>>>>> journal = BTjacs,
>>>>>> year = 1982,
>>>>>> volume = 104,
>>>>>> pages = "4546-4559"
>>>>>> }
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Paymon
>>>>>>>
>>>>>>>
>>>>>>> On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
>>>>>>>>> Message: 2
>>>>>>>>> Date: Wed, 22 Sep 2010 12:07:27 -0600
>>>>>>>>> From: Paymon Pirzadeh<ppirzade at ucalgary.ca>
>>>>>>>>> Subject: [gmx-users] rotational correlation function
>>>>>>>>> To: gmx-users at gromacs.org
>>>>>>>>> Message-ID:<1285178847.11669.66.camel at paymon-desktop>
>>>>>>>>> Content-Type: text/plain
>>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>> Imagine if the total correlation function of a protein could be
>>>>>>>>> factorized into rotational and internal portions:
>>>>>>>>> Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t)
>>>>>>>>> and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)?
>>>>>>>>> What does the g_rms -fit do? I am confused on how I can use gromacs
>>>>>>>>> commands on my output files. Sorry for mass of e-mails.
>>>>>>>>>
>>>>>>>>> Paymon
>>>>>>>>
>>>>>>>>
>>>>>>>> Hey, Paymon -
>>>>>>>>
>>>>>>>> Do you mean the correlation function of the velocity (VACF)? Why not
>>>>>>>> to use g_velacc and g_rotacf for translational and rotational VACFs? I
>>>>>>>> suppose, your molecule is rigid (enough) for rotational velocoty to
>>>>>>>> make sense.
>>>>>>>>
>>>>>>>> --
>>>>>>>> Dr. Vitaly V. Chaban
>>>>>>>> Department of Chemistry
>>>>>>>> University of Rochester
>>>>>>>> Rochester, NY 14627-0216
>>>>>>>> United States of America
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>> Dept. of Cell& Molec. Biol., Uppsala University.
>>>>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>>>>>
>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Dept. of Cell& Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell& Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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