[gmx-users] Re: rotational correlation function

[David van der Spoel]

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