[gmx-users] why rotational correlation function decays to negative

[Jennifer Vo]

Dear Tsjerk,
Many thanks for a very clear answer!
Regards,
Jennifer

On Wed, Mar 4, 2015 at 4:22 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Jennifer,
>
> The rotational autocorrelation looks at the correlation of the
> direction/extent of rotation as a function of time interval. The
> probability that it is going a certain way and still goes that direction a
> bit after is pretty large, so you get a positive correlation. A negative
> correlation means that, when you see it rotating one way at some time t,
> then, on average, you'll see it rotating the opposite direction after that
> interval of time. This may indicate that there are harmonic motions
> involved.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Mar 4, 2015 at 11:01 AM, Jennifer Vo <quyviolet at gmail.com> wrote:
>
> > Dear All,
> > I calculated rotational correlation function by g_rotacf and saw the
> > autocorrelation function started at 1 for t=0 and then decayed to 0 at
> > t=35ns then continued to negative numbers (-0.2, -0.4, -0.5 at t-50ns).
> > This is the command I use
> >  g_rotacf -s md_pro1_1st.tpr -n index.ndx -f md_pro1.xtc -o
> rotacf_pro1.xvg
> > -P 1
> >
> > This is the index.ndx
> > [ C-alpha_&_r_76_r_93 ]
> > 1076 1337
> > [ Backbone_&_r_76_r_93 ]
> > 1074 1076 1086 1335 1337 1340
> >
> > I try to calculate rotational correlation function of backbone and/or
> > C_alpha (with -d in g_rotacf) between two residues 76 and 93 (the longest
> > alpha helix in protein). So the negative number meant something wrong
> with
> > my simulation or with the calculation?
> > I would appreciate for any help.
> > Regards,
> > Jennifer
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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