[gmx-users] Re: rotational correlation function

[Paymon Pirzadeh]

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.

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