[gmx-users] Re: rotational correlation function

[Paymon Pirzadeh]

Great tips and advices. I appreciate your attention.
But, what would the g_rms -fit rot+trans  do? 

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