[gmx-users] Re: rotational correlation function

Paymon Pirzadeh ppirzade at ucalgary.ca
Thu Sep 23 18:14:19 CEST 2010


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?

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?

3. How can we generate a trajectory with no internal motions? Does it
have anything to do with g_rms?

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




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