[gmx-users] Re: rotational correlation function

[David van der Spoel]

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