[gmx-users] Re: rotational correlation function

[Vitaly Chaban]

> 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