[gmx-users] Re: rotational correlation function

Thu Sep 23 21:10:12 CEST 2010

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?
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