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

[Tsjerk Wassenaar]

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.